Package 'coMET'

Description

coMET is an R package for visualising EWAS results in a genomic region. Along with phenotype-association plots, coMET also generates plots of co-methylation patterns and provides a series of annotation tracks. The software is designed for epigenetic data, but can also be applied to genomic and functional genomic datasets (other omic-WAS results) in any species.

Details

coMET is an R package that can generate regional plots of EWAS results, DNA co-methylation patterns, and genomic information. A coMET figure includes 3 panels with a plot of P-values from EWAS, customized annotation tracks, and a triangle heatmap plot which demonstrates the correlation structure of DNA methylation at the CpG sites in the genomic region. Plots are created as PDF or EPS files.

Author(s)

Tiphaine C. Martin, Thomas Hardiman, Idil Yet, Pei-Chien Tsai, Jordana T. Bell

Maintainer: Tiphaine Martin <[email protected]>

Website: http://www.epigen.kcl.ac.uk/comet

References

Martin, T.C, Yet, I, Tsai, P-C, Bell, J.T., coMET: visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns, BMC bioinformatics, 2015.

Examples

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
configfile <- file.path(extdata, "config_cyp1b1_zoom_4comet.txt")
myinfofile <- file.path(extdata, "cyp1b1_infofile.txt")
myexpressfile <- file.path(extdata, "cyp1b1_infofile_exprGene_region.txt")
mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt")

chrom <- "chr2"
start <- 38290160
end <- 38303219
gen <- "hg38"

if(interactive()){
    genetrack <-genes_ENSEMBL(gen,chrom,start,end,showId=TRUE)
    snptrack <- snpBiomart_ENSEMBL(gen, chrom, start, end,
                dataset="hsapiens_snp_som",showId=FALSE)
    strutrack <- structureBiomart_ENSEMBL(gen, chrom, start, end,
                strand, dataset="hsapiens_structvar_som")
    clinVariant<-ClinVarMain_UCSC(gen,chrom,start,end)
    clinCNV<-ClinVarCnv_UCSC(gen,chrom,start,end)
    gwastrack <-GWAScatalog_UCSC(gen,chrom,start,end)
    geneRtrack <-GeneReviews_UCSC(gen,chrom,start,end)
    listgviz <- list(genetrack,snptrack,strutrack,clinVariant,
                 clinCNV,gwastrack,geneRtrack)
    comet(config.file=configfile, mydata.file=myinfofile, mydata.type="file",
      cormatrix.file=mycorrelation, cormatrix.type="listfile",
      mydata.large.file=myexpressfile, mydata.large.type="listfile",
      tracks.gviz=listgviz, verbose=FALSE, print.image=FALSE,disp.pvalueplot=FALSE)
} else {
    data(geneENSEMBLtrack)
    data(snpBiomarttrack)
    data(ISCAtrack)
    data(strucBiomarttrack)
    data(ClinVarCnvTrack)
    data(clinVarMaintrack)
    data(GWASTrack)
    data(GeneReviewTrack)

    listgviz <- list(genetrack,snptrack,strutrack,clinVariant,
                    clinCNV,gwastrack,geneRtrack)
    comet(config.file=configfile, mydata.file=myinfofile, mydata.type="listfile",
        cormatrix.file=mycorrelation, cormatrix.type="listfile",
        mydata.large.file=myexpressfile, mydata.large.type="listfile",
        tracks.gviz=listgviz,
        verbose=FALSE, print.image=FALSE,disp.pvalueplot=TRUE)
}

Description

Creates a binding motif track from ENSEMBL using the Gviz bioconductor package. A complete list of features and their associated colours can be found in the user guide.

Usage

bindingMotifsBiomart_ENSEMBL(gen, chr, start, end, featureDisplay="all",
datasetEnsembl = NULL, title="Binding Motifs ENSEMBL")

Arguments

Value

An AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

Tom Hardiman

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

Got to ENSEMBLregulation binding motif biomart

Examples

library("Gviz")
gen <- "hg38"
chr <- "chr1"
start <- 10000
end <- 50000
featureDisplay <- "CTCF"

if(interactive()){
 bindMotifsBiomartTrackSingle<-bindingMotifsBiomart_ENSEMBL(gen,chr,start,
 end,featureDisplay)
  plotTracks(bindMotifsBiomartTrackSingle, from = start, to = end,
  fontfamily="sans",fontfamily.title="sans")
} else {
  data(bindMotifsBiomartTrackSingle)
  plotTracks(bindMotifsBiomartTrackSingle, from = start, to = end,
  fontfamily="sans",fontfamily.title="sans")
}

######

library("Gviz")
gen <- "hg38"
chr <- "chr1"
start <- 10000
end <- 50000
featureDisplay <- c("CTCF","Egr1")

if(interactive()){
 bindMotifsBiomartTrackMultiple<-bindingMotifsBiomart_ENSEMBL(gen,chr,start,end,featureDisplay)
  plotTracks(bindMotifsBiomartTrackMultiple, from = start, to = end,
  fontfamily="sans",fontfamily.title="sans")
} else {
  data(bindMotifsBiomartTrackMultiple)
  plotTracks(bindMotifsBiomartTrackMultiple, from = start, to = end,
  fontfamily="sans",fontfamily.title="sans")
}

######

library("Gviz")
gen <- "hg38"
chr <- "chr1"
start <- 10000
end <- 50000
featureDisplay <- "all"

if(interactive()){
 bindMotifsBiomartTrackAll<-bindingMotifsBiomart_ENSEMBL(gen,chr,start,end,featureDisplay)
  plotTracks(bindMotifsBiomartTrackAll, from = start, to = end,
  fontfamily="sans",fontfamily.title="sans")
} else {
  data(bindMotifsBiomartTrackAll)
  plotTracks(bindMotifsBiomartTrackAll, from = start, to = end,
  fontfamily="sans",fontfamily.title="sans")
}

Description

Creates a track of TF motifs from ENCODE using the Gviz bioconductor package. A complete list of features and their associated colours can be found in the user guide.

Usage

ChIPTF_ENCODE(gen="hg19", chr, start, end, bedFilePath,
featureDisplay='all', motifColorFile, type_stacking='dense',
showId=FALSE,just_group="above", title="TF motifs ENCODE")

Arguments

Value

An AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

Got to BindingMotifsBiomart binding motif biomart

Examples

library("Gviz")
gen <- "hg19"
chr<-"chr1"
start <- 1000
end <- 329000


if(interactive()){
    extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
    bedFilePath <- file.path(extdata, "ENCODE/motifs1000_matches_ENCODE.txt")
    motif_color <- file.path(extdata, "ENCODE/TFmotifs_colors.csv")
    chipTFtrack <- ChIPTF_ENCODE(gen,chr,start, end, bedFilePath,
    featureDisplay=c("AHR::ARNT::HIF1A_1","AIRE_1","AIRE_2","AHR::ARNT_1"),
    motif_color,type_stacking="squish",showId=TRUE)
    plotTracks(chipTFtrack, from = start, to = end,
  fontfamily="sans",fontfamily.title="sans")
} else {
    data(chipTFtrack)
    plotTracks(chipTFtrack, from = start, to = end,
  fontfamily="sans",fontfamily.title="sans")
}

Description

Create multiple chromHMM Broad tracks by connecting to the UCSC genome browser using the GViz bioconductor package

Usage

chromatinHMMAll_UCSC(gen, chr, start, end, mySession, color='coMET',
pattern = NULL, table.name = NULL)

Arguments

Value

list of AnnotationTrack objects of GViz

Author(s)

Tiphaine Martin

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=wgEncodeHistoneSuper

See Also

chromatinHMMOne_UCSC

Examples

library("Gviz")
    library(rtracklayer)
    gen <- "hg19"
    chr <- "chr2"
    start <- 38290160
    end <- 38313219
    if(interactive()){
        BROWSER.SESSION="UCSC"
        mySession <- browserSession(BROWSER.SESSION)
        genome(mySession) <- gen
        track.name="Broad ChromHMM"
        tablestrack<-ucscTables(gen, track=track.name)
        table.name<-tablestrack[1]
        PATTERN.REGULATION<-"GM12878"

        chromhmmPattern<-chromatinHMMAll_UCSC(gen,chr,start,end,mySession,
        color='coMET',PATTERN.REGULATION)
        plotTracks(chromhmmPattern, from = start, to =end,
  fontfamily="sans",fontfamily.title="sans")

        chromhmmNoPattern<-chromatinHMMAll_UCSC(gen,chr,start,end,
        mySession,color='coMET')
        plotTracks(chromhmmNoPattern, from = start, to =end,
  fontfamily="sans",fontfamily.title="sans")
    } else {

        data(chromhmmPattern)
        plotTracks(chromhmmPattern, from = start, to =end,
  fontfamily="sans",fontfamily.title="sans")

        data(chromhmmNoPattern)
        plotTracks(chromhmmNoPattern, from = start, to =end,
  fontfamily="sans",fontfamily.title="sans")
    }

Description

Create one track of only one type of chromHMM Broad element from the UCSC genome browser using the Gviz bioconductor package

Usage

chromatinHMMOne_UCSC(gen, chr, start, end, mySession, color="coMET",
title="ENCODE/Broad chromHMM", table.name = NULL)

Arguments

Value

An AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

Tom Hardiman

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=wgEncodeHistoneSuper

See Also

chromatinHMMAll_UCSC

Examples

library("Gviz")
    library("rtracklayer")
    gen <- "hg19"
    chr <- "chr2"
    start <- 38290160
    end <- 38303219
    color <- "coMET"

    if(interactive()) {
        BROWSER.SESSION="UCSC"
        mySession <- browserSession(BROWSER.SESSION)
        genome(mySession) <- gen
        track.name="Broad ChromHMM"
        tablestrack<-ucscTables(gen, track.name)
        table.name<-tablestrack[1]
        chromhmmtrackone<-chromatinHMMOne_UCSC(gen,chr,start,end
        ,mySession,color="coMET",table.name)
        plotTracks(chromhmmtrackone, from = start, to =end,
  fontfamily="sans",fontfamily.title="sans")
    }else {
        data(chromhmmtrackone)
        plotTracks(chromhmmtrackone, from = start, to =end,
  fontfamily="sans",fontfamily.title="sans")
    }

Description

Creates a ChromHMM track from a file of RoadMap using the Gviz bioconductor package. A complete list of features and their associated colours can be found in the user guide.

Usage

chromHMM_RoadMap(gen="hg19",chr, start, end, bedFilePath,
featureDisplay = 'all', colorcase='roadmap15',
title=" chromHMM RoadMap")

Arguments

Value

An AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

Tom Hardiman

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

Got to RoadMap Epigenome

Examples

library("Gviz")
chr <- "chr1"
start <- 4500000
end <- 4600000
featureDisplay <- "7_Enh"

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
bedFilePath <- file.path(extdata, "RoadMap/E063_15_coreMarks_mnemonics.bed")

if(interactive()){
  chromHMM_RoadMapSingle <- chromHMM_RoadMap(gen="hg19",chr,start, end,
  bedFilePath, featureDisplay = featureDisplay, colorcase='roadmap15' )
  plotTracks(chromHMM_RoadMapSingle, from = start, to = end,
  fontfamily="sans",fontfamily.title="sans")
} else {
  data(chromHMM_RoadMapSingle)
  plotTracks(chromHMM_RoadMapSingle, from = start, to = end,
  fontfamily="sans",fontfamily.title="sans")
}

######

library("Gviz")
chr <- "chr22"
start <- 38291000
end <- 38301200
featureDisplay <- c("7_Enh","13_ReprPC")

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
bedFilePath <- file.path(extdata, "RoadMap/E063_15_coreMarks_mnemonics.bed")

if(interactive()){
  chromHMM_RoadMapMultiple <- chromHMM_RoadMap(gen="hg19",chr,start, end,
  bedFilePath, featureDisplay = featureDisplay, colorcase='roadmap15' )
  plotTracks(chromHMM_RoadMapMultiple, from = start, to = end,
  fontfamily="sans",fontfamily.title="sans")
} else {
  data(chromHMM_RoadMapMultiple)
  plotTracks(chromHMM_RoadMapMultiple, from = start, to = end,
  fontfamily="sans",fontfamily.title="sans")
}

#####

library("Gviz")
chr <- "chr22"
start <- 38291000
end <- 38301200
featureDisplay <- "all"

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
bedFilePath <- file.path(extdata, "RoadMap/E063_15_coreMarks_mnemonics.bed")

if(interactive()){
  chromHMM_RoadMapAll <- chromHMM_RoadMap(gen="hg19",chr,start, end,
  bedFilePath, featureDisplay = featureDisplay, colorcase='roadmap15' )
  plotTracks(chromHMM_RoadMapAll, from = start, to = end,
  fontfamily="sans",fontfamily.title="sans")
} else {
  data(chromHMM_RoadMapAll)
  plotTracks(chromHMM_RoadMapAll, from = start, to = end,
  fontfamily="sans",fontfamily.title="sans")
}

Description

Removing "chr" at the beginning of the chromosome number

Usage

chrUCSC2ENSEMBL(chr)

Arguments

Value

the number of chromosome at ENSEMBL format

Author(s)

Tiphaine Martin

Examples

chr<-"chr7"
    chrUCSC2ENSEMBL(chr)

Description

Create one track of the genomic positions of variants from the ClinVar database (CNV only, Variants excluded) using the Gviz bioconductor package

Usage

ClinVarCnv_UCSC(gen, chr, start, end, title="ClinVar Variants", showId = FALSE)

Arguments

Value

An UcscTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=clinvar

http://bioconductor.org/packages/release/bioc/html/Gviz.html

See Also

snpLocations_UCSC, structureBiomart_ENSEMBL, snpBiomart_ENSEMBL, CoreillCNV_UCSC, COSMIC_UCSC, ClinVarMain_UCSC

Examples

library("Gviz")
chrom <- "chr2"
start <- 38290160
end <- 38303219
gen <- "hg38"
if(interactive()){
    clinCNV<-ClinVarCnv_UCSC(gen,chrom,start,end)
    plotTracks(clinCNV, from = start, to =end,
    fontfamily="sans",fontfamily.title="sans")
}else {
    data(ClinVarCnvTrack)
    plotTracks(clinCNV, from = start, to =end,
             fontfamily="sans",fontfamily.title="sans")
}

Description

Create one track of the genomic positions of variants from the ClinVar database (Variants only, CNV excluded) using the Gviz bioconductor package

Usage

ClinVarMain_UCSC(gen, chr, start, end, title="ClinVar Variants", showId=FALSE)

Arguments

Value

An UcscTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=clinvar

http://bioconductor.org/packages/release/bioc/html/Gviz.html

See Also

snpLocations_UCSC, structureBiomart_ENSEMBL, snpBiomart_ENSEMBL, CoreillCNV_UCSC, COSMIC_UCSC, ClinVarCnv_UCSC

Examples

library("Gviz")
gen <- "hg38"
chrom <- "chr2"
start <- 100000
end <- 10000000

if(interactive()) {
    clinVariant<-ClinVarMain_UCSC(gen,chrom,start,end)
    plotTracks(clinVariant, from = start, to =end,
    fontfamily="sans",fontfamily.title="sans")
}else{
    data(clinVarMaintrack)
    plotTracks(clinVariant, from = start, to =end,
    fontfamily="sans",fontfamily.title="sans")
}

Description

col2HSV converts an R color (or a set of colors) into an HSV color model, and then returns the color names in hexadeciaml notation

Usage

col2HSV(color)

Arguments

Value

A character vector with the color(s) name(s) in hexadecimal notation

Author(s)

Gaston Sanchez

Examples

# convert 'tomato'
col2HSV("tomato")

Description

coMET is an R-based package to visualize EWAS (epigenome-wide association scans) results in a genomic region of interest. The main feature of coMET is to plot the the significance level of EWAS results in the selected region, along with correlation in DNA methylation values between CpG sites in the region. The coMET package generates plots of phenotype-association, co-methylation patterns, and a series of annotation tracks.

Usage

comet(mydata.file = NULL, mydata.format = "site", mydata.type = "file",
    mydata.large.file = NULL, mydata.large.format = "site",
    mydata.large.type = "listfile", cormatrix.file = NULL,
    cormatrix.method = "spearman", cormatrix.format = "raw",
    cormatrix.color.scheme = "bluewhitered",cormatrix.conf.level=0.05,
    cormatrix.sig.level= 1, cormatrix.adjust="none",
    cormatrix.type = "listfile", mydata.ref = NULL,
    start = NULL, end = NULL, zoom = FALSE, lab.Y = "log",
    pval.threshold = 1e-05,pval.threshold.2 = 0,disp.pval.threshold = 1,
    disp.association = FALSE, disp.association.large = FALSE,
    disp.region = FALSE, disp.region.large = FALSE,
    disp.beta.association = FALSE, disp.beta.association.large = FALSE, factor.beta = 0.3,
    symbols = "circle-fill",
    symbols.large = NA, sample.labels = NULL, sample.labels.large = NULL,
    use.colors = TRUE , disp.color.ref = TRUE, color.list = NULL, color.list.large = NULL,
    disp.mydata = TRUE, biofeat.user.file = NULL, biofeat.user.type = NULL,
    biofeat.user.type.plot = NULL,
    genome = "hg19", dataset.gene = "hsapiens_gene_ensembl",
    tracks.gviz = NULL,
    disp.mydata.names = TRUE, disp.color.bar = TRUE, disp.phys.dist = TRUE,
    disp.legend = TRUE, disp.marker.lines = TRUE, disp.cormatrixmap = TRUE,
    disp.pvalueplot =TRUE, disp.type = "symbol", disp.mult.lab.X = FALSE,
    disp.connecting.lines = TRUE, palette.file = NULL, image.title = NULL,
    image.name = "coMET", image.type = NULL, image.size = 3.5,
    fontsize.gviz=5, font.factor = 1,
    symbol.factor = NULL, print.image = TRUE, connecting.lines.factor = 1.5,
    connecting.lines.adj = 0.01, connecting.lines.vert.adj = -1,
    connecting.lines.flex = 0, config.file = NULL, verbose = FALSE)

Arguments

Details

The function is limited to visualize 120 omic features.

Value

Create a plot in pdf or eps format depending to some options

Author(s)

Tiphaine Martin

References

http://epigen.kcl.ac.uk/comet/

See Also

comet.web,comet.list

Examples

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
configfile <- file.path(extdata, "config_cyp1b1_zoom_4comet.txt")
myinfofile <- file.path(extdata, "cyp1b1_infofile.txt")
myexpressfile <- file.path(extdata, "cyp1b1_infofile_exprGene_region.txt")
mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt")

chrom <- "chr2"
start <- 38290160
end <- 38303219
gen <- "hg38"

if(interactive()){
    cat("interactive")
    genetrack <-genes_ENSEMBL(gen,chrom,start,end,showId=TRUE)
    snptrack <- snpBiomart_ENSEMBL(gen, chrom, start, end,
                dataset="hsapiens_snp_som",showId=FALSE)
    strutrack <- structureBiomart_ENSEMBL(gen, chrom, start, end,
                strand, dataset="hsapiens_structvar_som")
    clinVariant<-ClinVarMain_UCSC(gen,chrom,start,end)
    clinCNV<-ClinVarCnv_UCSC(gen,chrom,start,end)
    gwastrack <-GWAScatalog_UCSC(gen,chrom,start,end)
    geneRtrack <-GeneReviews_UCSC(gen,chrom,start,end)
    listgviz <- list(genetrack,snptrack,strutrack,clinVariant,
                 clinCNV,gwastrack,geneRtrack)
    comet(config.file=configfile, mydata.file=myinfofile, mydata.type="file",
      cormatrix.file=mycorrelation, cormatrix.type="listfile",
      mydata.large.file=myexpressfile, mydata.large.type="listfile",
      tracks.gviz=listgviz, verbose=FALSE, print.image=FALSE,disp.pvalueplot=FALSE)
} else {
    cat("Non interactive")
    data(geneENSEMBLtrack)
    data(snpBiomarttrack)
    data(ISCAtrack)
    data(strucBiomarttrack)
    data(ClinVarCnvTrack)
    data(clinVarMaintrack)
    data(GWASTrack)
    data(GeneReviewTrack)
    listgviz <- list(genetrack,snptrack,strutrack,clinVariant,
                clinCNV,gwastrack,geneRtrack)
    comet(config.file=configfile, mydata.file=myinfofile, mydata.type="file",
       cormatrix.file=mycorrelation, cormatrix.type="listfile",
        mydata.large.file=myexpressfile,  mydata.large.type="listfile",
        tracks.gviz=listgviz, verbose=FALSE, print.image=FALSE,disp.pvalueplot=FALSE)
}

Description

coMET is an R-based package to visualize EWAS (epigenome-wide association scans) results in a genomic region of interest. The main feature of coMET is to plot the the significance level of EWAS results in the selected region, along with correlation in DNA methylation values between CpG sites in the region. The coMET package generates plots of phenotype-association, co-methylation patterns, and a series of annotation tracks. In addition, the function comet.list gives the list of correlations between omic features

Usage

comet.list(cormatrix.file = NULL, cormatrix.method = "spearman", cormatrix.format = "raw",
    cormatrix.conf.level=0.05, cormatrix.sig.level= 1, cormatrix.adjust="none",
    cormatrix.type = "listdataframe", cormatrix.output="cormatrix_list",
    config.file = NULL, verbose = FALSE)

Arguments

Value

Create a list of correlation between omic features

Author(s)

Tiphaine Martin

References

http://epigen.kcl.ac.uk/comet/

See Also

comet.web,comet

Examples

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt")
myoutput <- file.path(extdata, "cyp1b1_res37_cormatrix_list_BH05.txt")


comet.list(cormatrix.file=mycorrelation,cormatrix.method = "spearman",
           cormatrix.format= "raw", cormatrix.conf.level=0.05,
           cormatrix.sig.level= 0.05, cormatrix.adjust="BH",
           cormatrix.type = "listfile", cormatrix.output=myoutput,
           verbose=FALSE)

Description

coMET is an R-based package to visualize EWAS (epigenome-wide association scans) results in a genomic region of interest. The main feature of coMET is to plot the the significance level of EWAS results in the selected region, along with correlation in DNA methylation values between CpG sites in the region. The coMET package generates plots of phenotype-association, co-methylation patterns, and a series of annotation tracks.

Usage

comet.web(mydata.file = NULL, mydata.format = c("site", "region",
"site_asso", "region_asso"),
        mydata.large.file = NULL,
        mydata.large.format = c("site", "region", "site_asso", "region_asso"),
        cormatrix.file = NULL, cormatrix.method = c("spearman", "pearson", "kendall"),
        cormatrix.format = c("cormatrix", "raw","raw_rev"),
        cormatrix.color.scheme = "heat", cormatrix.conf.level=0.05,
        cormatrix.sig.level= 1, cormatrix.adjust="none",mydata.ref = NULL,
        genome="hg19", start = NULL, end = NULL, zoom = FALSE, lab.Y = "log",
        pval.threshold = 1e-07, pval.threshold.2 = 0,  disp.pval.threshold = 1,
        disp.association= FALSE, disp.association.large = FALSE,
        disp.beta.association = "FALSE", disp.beta.association.large = "FALSE",
        factor.beta = 0.3,
        disp.region = FALSE, disp.region.large = FALSE, symbols = "circle-fill",
        symbols.large = NA, sample.labels = NULL, sample.labels.large = NULL,
        use.colors = TRUE, disp.color.ref = TRUE, color.list = NULL,
        color.list.large = NULL, biofeat.user.file = NULL,
        biofeat.user.type = c("GeneRegion", "Annotation", "Data"),
        biofeat.user.type.plot = NULL,
        list.tracks = "geneENSEMBL,CGI,ChromHMM,DNAse,RegENSEMBL,SNP",
        pattern.regulation = "GM12878",
        image.title = NULL, image.name = "coMET", image.type = c("pdf", "eps"),
        image.size = 3.5, fontsize.gviz=5, font.factor = 1,
        print.image = FALSE, config.file = NULL, verbose = FALSE)

Arguments

.

Details

The function is limited to visualize 120 omic features.

Value

Create a plot in pdf or eps format depending to some options

Author(s)

Tiphaine Martin

References

http://epigen.kcl.ac.uk/comet/

See Also

comet,comet.list

Examples

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
configfile <- file.path(extdata, "config_cyp1b1_zoom_4webserver.txt")
myinfofile <- file.path(extdata, "cyp1b1_infofile.txt")
myexpressfile <- file.path(extdata, "cyp1b1_infofile_exprGene_region.txt")
mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt")

comet.web(config.file=configfile, mydata.file=myinfofile, cormatrix.file=mycorrelation,
    mydata.large.file=myexpressfile, print.image=FALSE,verbose=FALSE)

Description

Complementary or opposite color scheme is formed by colors that are opposite each other on the color wheel (example: red and green). The high contrast of complementary colors creates a vibrant look that must be managed well so it is not jarring.

Usage

complementary(color, plot = TRUE, bg = "white",
    labcol = NULL, cex = 0.8, title = TRUE)

Arguments

Details

The complementary color is obtained following a color wheel with 12 colors, each one spaced at 30 degrees from each other. Complementary color schemes are tricky to use in large doses, but work well when you wnat something to stand out. In addition, omplementary colors are really bad for text.

Value

A character vector with the given color and the complementary color in hexadecimal notation

Author(s)

Gaston Sanchez

Examples

# complementary color of 'tomato' with no plot
opposite("tomato", plot = FALSE)

# complementary color of 'tomato' with color wheel
opposite("tomato", bg = "gray30")

Description

Create one track of the genomic positions of copy-number variants (CNVs) in chromosomal aberration and inherited disorder cell lines from the NIGMS Human Genetic Cell Repository using the Gviz bioconductor package.

Usage

CoreillCNV_UCSC(gen, chr, start, end,title="Coriell CNVs", showId=FALSE)

Arguments

Value

An UcscTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=coriellDelDup

See Also

snpLocations_UCSC, structureBiomart_ENSEMBL, snpBiomart_ENSEMBL, COSMIC_UCSC, ClinVarMain_UCSC, ClinVarCnv_UCSC

Examples

library("Gviz")
gen <- "hg19"
chrom <- "chr2"
start <- 38290160
end <- 38303219

if(interactive()){
    coreilVariant<-CoreillCNV_UCSC(gen,chrom,start,end)
    plotTracks(coreilVariant, from = start, to =end,
    fontfamily="sans",fontfamily.title="sans")
} else {
     data(coreilVarianttrack)
    plotTracks(coreilVariant, from = start, to =end,
    fontfamily="sans",fontfamily.title="sans")
}

Description

[obselete] No more possible to extract COSMIC data from UCSC.

Create one track of the genomic positions of variants from COSMIC, the "Catalogue Of Somatic Mutations In Cancer" in extracting data from UCSC and using the Gviz bioconductor package.

Usage

COSMIC_UCSC(gen, chr, start, end,title= "COSMIC", showId=FALSE)

Arguments

Value

An UcscTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=cosmic

See Also

snpLocations_UCSC, structureBiomart_ENSEMBL, snpBiomart_ENSEMBL, CoreillCNV_UCSC, ClinVarMain_UCSC, ClinVarCnv_UCSC,

Examples

library("Gviz")
chrom <- "chr2"
start <- 38290160
end <- 38303219
gen <- "hg19"
if(interactive()){
    cosmicVariant<-COSMIC_UCSC(gen,chrom,start,end)
    plotTracks(cosmicVariant, from = start, to =end,
    fontfamily="sans",fontfamily.title="sans")
}else {
    data(cosmicVarianttrack)
    plotTracks(cosmicVariant, from = start, to =end,
    fontfamily="sans",fontfamily.title="sans")
}

Description

create track CpG Island from UCSC using the Gviz bioconductor package

Usage

cpgIslands_UCSC(gen, chr, start, end, title="CpG Islands UCSC")

Arguments

Value

An UcscTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=cpgIslandSuper

Examples

library("Gviz")
chrom <- "chr2"
start <- 100000
end <- 1000000
gen <- "hg38"

if(interactive()) {
    cpgIstrack<-cpgIslands_UCSC(gen, chrom, start, end)
    plotTracks(cpgIstrack, from = start, to =end,
    fontfamily="sans",fontfamily.title="sans")
}else {
    data(cpgIslandtrack)
    plotTracks(cpgIstrack, from = start, to =end,
    fontfamily="sans",fontfamily.title="sans")
}

Description

Creates a DGFP track from a file of RoadMap using the Gviz bioconductor package. A complete list of features and their associated colours can be found in the user guide.

Usage

dgfootprints_RoadMap(gen="hg19", chr, start, end, bedFilePath,
tissueGroupDisplay='Blood & T-cell',showId=FALSE, type_stacking="dense",
title= "DGFP RoadMap")

Arguments

Value

An AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

Tom Hardiman

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

Got to RoadMap Epigenome

Examples

library("Gviz")
chr <- "chr1"
start <- 236728
end <- 238778
gen="hg19"

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
bedFilePath <- file.path(extdata, "RoadMap/CD3-DS17198.hg19_subset.bed")

if(interactive()){
  dgfootprints_RoadMapSingle <- dgfootprints_RoadMap(gen,chr,start, end,
  bedFilePath, tissueGroupDisplay='Blood & T-cell' )
  plotTracks(dgfootprints_RoadMapSingle, from = start, to = end,
    fontfamily="sans",fontfamily.title="sans")
} else {
  data(dgfootprints_RoadMapSingle)
  plotTracks(dgfootprints_RoadMapSingle, from = start, to = end,
    fontfamily="sans",fontfamily.title="sans")
}

Description

Creation of DNase cluster track from a connection to UCSC genome browser in using the GViz bioconductor package. Obselete function

Usage

DNAse_UCSC(gen, chr, start, end, mySession, title="DNA cluster",
track.name = "DNase Clusters", table.name = NULL)

Arguments

Value

An AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=wgEncodeDNAseSuper

Examples

# library("Gviz")
# library("rtracklayer")

# gen <- "hg19"
# chr <- "chr7"
# start <- 38290160
# end <- 38303219
# if(interactive()){
#   BROWSER.SESSION="UCSC"
#   mySession <- browserSession(BROWSER.SESSION)
#   genome(mySession) <- gen
#   track.name="Broad ChromHMM"
#   tablestrack<-tableNames(ucscTableQuery(mySession, track=track.name))
#   table.name<-tablestrack[1]
#   dnasetrack<-DNAse_UCSC(gen,chr,start,end,mySession)
#   plotTracks(dnasetrack, from = start, to =end,
#                                   fontfamily="sans",fontfamily.title="sans")
# }else {
#     data(dnasetrack)
#    plotTracks(dnasetrack, from = start, to =end,
#                                   fontfamily="sans",fontfamily.title="sans")
# }

Description

Creates a track of promoters/enhancers from FANTOM using the Gviz bioconductor package. A complete list of features and their associated colours can be found in the user guide.

Usage

DNaseI_FANTOM(gen="hg19", chr, start, end, bedFilePath,
featureDisplay='enhancer', stacking_type="dense",
title=" DNaseI Fantom")

Arguments

Value

An AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

Got to BindingMotifsBiomart binding motif biomart

Examples

library("Gviz")
gen <- "hg19"
chr<- "chr1"
start <- 6000000
end <- 6500000

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
enhFantomFile <- file.path(extdata,
"/FANTOM/human_permissive_enhancers_phase_1_and_2_example970.bed")

if(interactive()){
 enhFANTOMtrack <- DNaseI_FANTOM(gen,chr,start, end,
 enhFantomFile, featureDisplay='enhancer')
  plotTracks(enhFANTOMtrack, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(enhFANTOMtrack)
  plotTracks(enhFANTOMtrack, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
}

Description

Creates a track of promoter/enhancer regions from a file of RoadMap using the Gviz bioconductor package. A complete list of features and their associated colours can be found in the user guide.

Usage

DNaseI_RoadMap(gen="hg19", chr, start, end, bedFilePath,
featureDisplay='promotor',showId=TRUE, type_stacking="dense",
title = "DNaseI RoadMap")

Arguments

Value

An AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

Tom Hardiman

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

Got to RoadMap Epigenome

Examples

library("Gviz")
chr <- "chr2"
start <- 38300049
end <- 38302592
gen="hg19"

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
bedFilePath <- file.path(extdata, "RoadMap/regions_prom_E063.bed")

if(interactive()){
  DNaseI_RoadMapSingle <- DNaseI_RoadMap(gen,chr,start, end,
  bedFilePath, featureDisplay='promotor'  )
  plotTracks(DNaseI_RoadMapSingle, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(DNaseI_RoadMapSingle)
  plotTracks(DNaseI_RoadMapSingle, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
}

Description

Creates a track from a BED file for eQTL data using the Gviz bioconductor package. A complete list of features and their associated colours can be found in the user guide.

Usage

eQTL(gen,chr, start, end, bedFilePath, featureDisplay, showId=FALSE,
type_stacking="squish",just_group="above", title="eQTL" )

Arguments

Value

An AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

Tom Hardiman

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

Got to ENSEMBLregulation binding motif biomart

Examples

library("Gviz")
chr <- "chr15"
start <- 74889136
end <-   75018200
featureDisplay <- "SNP"
gen="hg19"

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
bedFilePath <- file.path(extdata, "eQTL.bed")

if(interactive()){
  eQTLTrackSingle <- eQTL(gen,chr,start, end, bedFilePath, 
  featureDisplay = featureDisplay )
  plotTracks(eQTLTrackSingle, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(eQTLTrackSingle)
  plotTracks(eQTLTrackSingle, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
}

###########

library("Gviz")
chr <- "chr15"
start <- 74889136
end <-   75018200
featureDisplay <- c("SNP","mRNA_pheno")
gen="hg19"

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
bedFilePath <- file.path(extdata, "eQTL.bed")

if(interactive()){
  eQTLTrackMultiple <- eQTL(gen,chr,start, end, bedFilePath, featureDisplay = featureDisplay )
  plotTracks(eQTLTrackMultiple, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(eQTLTrackMultiple)
  plotTracks(eQTLTrackMultiple, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
}

######

library("Gviz")
chr <- "chr15"
start <- 74889136
end <-   75018200
featureDisplay <- "all"
gen="hg19"

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
bedFilePath <- file.path(extdata, "eQTL.bed")

if(interactive()){
  eQTLTrackAll <- eQTL(gen,chr,start, end, bedFilePath, featureDisplay = featureDisplay )
  plotTracks(eQTLTrackAll, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(eQTLTrackAll)
  plotTracks(eQTLTrackAll, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
}

Description

Creates a track of eQTL from GTEx using the Gviz bioconductor package. A complete list of features and their associated colours can be found in the user guide.

Usage

eQTL_GTEx(gen="hg19",chr,start, end, bedFilePath, featureDisplay = 'all',
showId=FALSE, type_stacking="squish",just_group="above",title="eQTL GTEX")

Arguments

Value

An AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

Got to BindingMotifsBiomart binding motif biomart

Examples

library("Gviz")
gen <- "hg19"
chr<-"chr3"
start <- 132423172
end <- 132442807
extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
bedFilePath <- file.path(extdata, "/GTEX/eQTL_Uterus_Analysis_extract100.snpgenes")

if(interactive()){
 eGTexTrackall <- eQTL_GTEx(gen,chr,start, end, bedFilePath,
 featureDisplay="all", showId=TRUE,just_group="left")
  plotTracks(eGTexTrackall, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(eGTexTrackall)
  plotTracks(eGTexTrackall, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
}

if(interactive()){
 eGTexTrackSNP <- eQTL_GTEx(gen,chr,start, end, bedFilePath,
 featureDisplay="SNP", showId=TRUE,just_group="left")
  plotTracks(eGTexTrackSNP, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(eGTexTrackSNP)
  plotTracks(eGTexTrackSNP, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
}

Description

Create one track of the genomic positions of variants from the Genetic Association Database (GAD) (archive of human genetic association studies of complex diseases and disorders) using the Gviz bioconductor package

Usage

GAD_UCSC(gen, chr, start, end,title="GAD", showId=FALSE)

Arguments

Value

An UcscTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=gad

See Also

ISCA_UCSC, GWAScatalog_UCSC, knownGenes_UCSC, genesName_ENSEMBL, GeneReviews_UCSC, genes_ENSEMBL, xenorefGenes_UCSC, transcript_ENSEMBL,

Examples

library("Gviz")
gen2 <- "hg19"
chrom2 <- "chr2"
start2 <- 38290160
end2 <- 38303219

if(interactive()) {
  gadtrack<-GAD_UCSC(gen=gen2 ,chr=chrom2 ,start=start2 ,end=end2)
  plotTracks(gadtrack, from = start2, to =end2,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(gadtrack)
   plotTracks(gadtrack, from = start2, to =end2,
                                   fontfamily="sans",fontfamily.title="sans")
}

Description

Create a track of GC content from UCSC using the Gviz bioconductor package

Usage

gcContent_UCSC(gen, chr, start, end, title="GC Percent")

Arguments

Value

A UcscTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=gc5Base

Examples

library("Gviz")
gen <- "hg38"
chr <- "chr7"
start <- 38290160
end <- 38303219

if(interactive()){
  gctrack<-gcContent_UCSC(gen,chr,start,end)
  plotTracks(gctrack,from= start, to=end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(gctrack)
  plotTracks(gctrack,from= start, to=end,
                                   fontfamily="sans",fontfamily.title="sans")
}

Description

Create one track of the genomic positions of variants from GeneReviews using the Gviz bioconductor package

Usage

GeneReviews_UCSC(gen, chr, start, end,title="GeneReviews", showId=FALSE)

Arguments

Value

An UcscTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=geneReviews

See Also

ISCA_UCSC, GWAScatalog_UCSC, knownGenes_UCSC, genesName_ENSEMBL, GAD_UCSC, genes_ENSEMBL, xenorefGenes_UCSC, transcript_ENSEMBL,

Examples

library("Gviz")
gen <- "hg38"
chrom <- "chr2"
start <- 10000000
end <- 100000000
if(interactive()){
  geneRtrack <-GeneReviews_UCSC(gen,chrom,start,end,showId=TRUE)
  plotTracks(geneRtrack, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(GeneReviewTrack)
  plotTracks(geneRtrack, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
}

Description

Create one track of the genes in the genomic regions of interest from EMSEMBL using the Gviz bioconductor package

Usage

genes_ENSEMBL(gen, chr, start, end, showId=FALSE,title="genes (ENSEMBL)")

Arguments

Value

A BiomartGeneRegionTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=ensGene

See Also

ISCA_UCSC, GWAScatalog_UCSC, knownGenes_UCSC, genesName_ENSEMBL, GeneReviews_UCSC, GAD_UCSC, xenorefGenes_UCSC, transcript_ENSEMBL,

Examples

library("Gviz")
gen <- "hg19"
chrom <- "chr2"
start <- 38290160
end <- 38303219
if(interactive()) {
  genetrack <-genes_ENSEMBL(gen,chrom,start,end,showId=TRUE)
  plotTracks(genetrack, from = start, to =end,
  fontfamily="sans",fontfamily.title="sans")
} else {
  data(geneENSEMBLtrack)
  plotTracks(genetrack, from = start, to =end,
  fontfamily="sans",fontfamily.title="sans")
}

Description

Obtain the genes names in the genomic regions of interest from ENSEMBL

Usage

genesName_ENSEMBL(gen, chr, start, end, dataset)

Arguments

Details

Can be null

Value

List of name of genes found in this region of interest.

Author(s)

Tiphaine Martin

References

go to ENSEMBL

http://bioconductor.org/packages/release/bioc/html/Gviz.html

See Also

ISCA_UCSC, GWAScatalog_UCSC, knownGenes_UCSC, GeneReviews_UCSC, GAD_UCSC, genes_ENSEMBL, xenorefGenes_UCSC, transcript_ENSEMBL,

Examples

library("Gviz")
gen <- "hg38"
chr <- "chr7"
start <- 38290160
end <- 38303219

if(interactive()){
  dataset<- "hsapiens_gene_ensembl"
  geneNameEnsembl<- genesName_ENSEMBL(gen,chr,start,end,dataset)
  geneNameEnsembl
} else {
  data(geneNameEnsembl)
  geneNameEnsembl
}

Description

Create one track of the genomic positions of variants from the NHGRI Catalog of Published Genome-Wide Association Studies using the Gviz bioconductor package

Usage

GWAScatalog_UCSC(gen, chr, start, end, title="GWAS Catalog", showId=FALSE)

Arguments

Value

An UcscTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=gwasCatalog

http://bioconductor.org/packages/release/bioc/html/Gviz.html

See Also

ISCA_UCSC, knownGenes_UCSC, genesName_ENSEMBL, GeneReviews_UCSC, GAD_UCSC, genes_ENSEMBL, xenorefGenes_UCSC, transcript_ENSEMBL,

Examples

library("Gviz")
gen <- "hg38"
chrom <- "chr2"
start <- 10000
end <- 100000

if(interactive()) {
  gwastrack <-GWAScatalog_UCSC(gen,chrom,start,end)
  plotTracks(gwastrack, from = start, to =end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(GWASTrack)
  plotTracks(gwastrack, from = start, to =end,
                                   fontfamily="sans",fontfamily.title="sans")
}

Description

Creates a HiC matrix from Rao et al.,2014.

Usage

HiCdata2matrix( chr, start, end, bedFilePath)

Arguments

Value

An AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

Got to BindingMotifsBiomart binding motif biomart

Examples

library("corrplot")
gen <- "hg19"
chr<-"chr1"
start <- 5000000
end <- 9000000

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
bedFilePath <- file.path(extdata, "HiC/chr1_1mb.RAWobserved")

if(interactive()){
  matrix_HiC_Rao <- HiCdata2matrix(chr,start, end, bedFilePath)
cor_matrix_HiC <- cor(matrix_HiC_Rao)
diag(cor_matrix_HiC)<-1
corrplot(cor_matrix_HiC, method = "circle")
} else {
  data(matrix_HiC_Rao)
  cor_matrix_HiC <- cor(matrix_HiC_Rao)
diag(cor_matrix_HiC)<-1
corrplot(cor_matrix_HiC, method = "circle")
}

Description

Create multiple tracks of histone modifications from the UCSC genome browser (ENCODE/Broad) using the Gviz bioconductor package

Usage

HistoneAll_UCSC(gen, chr, start, end, mySession, pattern = NULL,
          track.name = "Broad Histone", table.name = NULL)

Arguments

Value

A list of AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=wgEncodeHistoneSuper

http://bioconductor.org/packages/release/bioc/html/Gviz.html

See Also

HistoneOne_UCSC,

Examples

library("Gviz")
library("rtracklayer")
gen <- "hg19"
chr <- "chr2"
start <- 38290160
end <- 38313219

if(interactive()){
  BROWSER.SESSION="UCSC"
  mySession <- browserSession(BROWSER.SESSION)
  genome(mySession) <- gen
  pattern1 <- "GM12878"

  histonalltrack<-HistoneAll_UCSC(gen,chr,start,end,mySession,
  pattern=pattern1,track.name="Broad Histone")
  plotTracks(histonalltrack, from = start, to =end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(histonalltrack)
  plotTracks(histonalltrack, from = start, to =end,
                                   fontfamily="sans",fontfamily.title="sans")
}

Description

Create one track of one histone modification profile from the UCSC genome browser (ENCODE/Broad) using the Gviz bioconductor package

Usage

HistoneOne_UCSC(gen, chr, start, end, mySession, title="Broad Histone",
track.name = "Broad Histone", table.name = NULL)

Arguments

Value

An AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=wgEncodeHistoneSuper

http://bioconductor.org/packages/release/bioc/html/Gviz.html

See Also

HistoneAll_UCSC

Examples

library("Gviz")
library("rtracklayer")
gen <- "hg19"
chr <- "chr2"
start <- 38290160
end <- 38303219

if(interactive()) {
  BROWSER.SESSION="UCSC"
  mySession <- browserSession(BROWSER.SESSION)
  genome(mySession) <- gen
  histoneonetrack<-HistoneOne_UCSC(gen,chr,start,end,mySession)
  plotTracks(histoneonetrack, from = start, to =end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(histoneonetrack)
  plotTracks(histoneonetrack, from = start, to =end,
                                   fontfamily="sans",fontfamily.title="sans")
}

Description

Creates a track of imprinted genes from GTEx using the Gviz bioconductor package. A complete list of features and their associated colours can be found in the user guide.

Usage

imprintedGenes_GTEx(gen="hg19", chr,start, end, tissues="all",
classification="all",showId=FALSE, title="Imprinted genes GTEx")

Arguments

Value

An AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

Got to BindingMotifsBiomart binding motif biomart

Examples

library("Gviz")
gen<-"hg19"
chr<- "chr6"
start <- 144251437
end <- 144330541

if(interactive()){
   allIGtrack <- imprintedGenes_GTEx(gen,chr,start, end,
   tissues="all", classification="imprinted",showId=TRUE)
   allimprintedIGtrack <- imprintedGenes_GTEx(gen,chr,start, end,
   tissues="all", classification="imprinted",showId=TRUE)
   StomachIGtrack <-imprintedGenes_GTEx(gen,chr,start, end,
   tissues="Stomach", classification="all",showId=TRUE)
   PancreasIGtrack <- imprintedGenes_GTEx(gen,chr,start, end,
   tissues="Pancreas", classification="all",showId=TRUE)
   PancreasimprintedIGtrack <- imprintedGenes_GTEx(gen,chr,start, end,
   tissues="Pancreas", classification="biallelic",showId=TRUE)

   imprintinglist <- list(allIGtrack,allimprintedIGtrack,
   StomachIGtrack,PancreasIGtrack,PancreasimprintedIGtrack)

  plotTracks(imprintinglist, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")

} else {

  data(allIGtrack)
  data(allimprintedIGtrack)
  data(StomachIGtrack)
  data(PancreasIGtrack)
  data(PancreasimprintedIGtrack)

   imprintinglist <- list(allIGtrack,allimprintedIGtrack,
   StomachIGtrack,PancreasIGtrack,PancreasimprintedIGtrack)

  plotTracks(imprintinglist, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
}

Description

Create one track of the genes in the genomic regions of interest from EMSEMBL using the Gviz bioconductor package

Usage

interestGenes_ENSEMBL(gen, chr, start, end, interestfeatures,interestcolor,
showId=FALSE,title="genes (ENSEMBL)")

Arguments

Value

A BiomartGeneRegionTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=ensGene

See Also

ISCA_UCSC, GWAScatalog_UCSC, knownGenes_UCSC, genesName_ENSEMBL, GeneReviews_UCSC, GAD_UCSC, xenorefGenes_UCSC, transcript_ENSEMBL,

Examples

library("Gviz")
gen <- "hg19"
chr <- "chr15"
start <- 75011669
end <- 75019876
interestfeatures <- rbind(c("75011883","75013394","bad"),c("75013932","75014410","good"))
interestcolor <- list("bad"="red", "good"="green")

if(interactive()) {
  interestgenesENSMBLtrack<-interestGenes_ENSEMBL(gen,chr,start,end,
  interestfeatures,interestcolor,showId=TRUE)
  plotTracks(interestgenesENSMBLtrack, from = start, to =end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(interestgenesENSMBLtrack)
  plotTracks(interestgenesENSMBLtrack, from = start, to =end,
                                   fontfamily="sans",fontfamily.title="sans")
}

Description

Create a track to visualize different transcripts from ENSEMBL using the Gviz bioconductor package

Usage

interestTranscript_ENSEMBL(gen, chr, start, end,interestfeatures,
interestcolor,showId = FALSE, title="transcripts ENSEMBL")

Arguments

Value

A BiomartGeneRegionTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=ensGene

See Also

ISCA_UCSC, GWAScatalog_UCSC, knownGenes_UCSC, genesName_ENSEMBL, GeneReviews_UCSC, GAD_UCSC, genes_ENSEMBL, xenorefGenes_UCSC,

Examples

library("Gviz")
gen <- "hg19"
chr <- "chr15"
start <- 75011669
end <- 75019876
interestfeatures <- rbind(c("75017782","75017835","bad"),c("75013755","75013844","good"))
interestcolor <- list("bad"="red", "good"="green")

if(interactive()){
  interesttransENSMBLtrack<-interestTranscript_ENSEMBL(gen,chr,start,end,
  interestfeatures,interestcolor,showId=TRUE)
  plotTracks(interesttransENSMBLtrack, from=start, to=end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(interesttransENSMBLtrack)
  plotTracks(interesttransENSMBLtrack, from=start, to=end,
                                   fontfamily="sans",fontfamily.title="sans")
}

Description

Create one track of the genomic positions of variants from International Standards for Cytogenomic Arrays (ISCA) Consortium using the Gviz bioconductor package (obselete datbase, Impossible to access to data from UCSC from September 2015)

Usage

ISCA_UCSC(gen, chr, start, end, mySession, table.name,title="ISCA", showId=FALSE)

Arguments

Value

An UcscTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=iscaComposite

http://bioconductor.org/packages/release/bioc/html/Gviz.html

See Also

GWAScatalog_UCSC, knownGenes_UCSC, genesName_ENSEMBL, GeneReviews_UCSC, GAD_UCSC, genes_ENSEMBL, xenorefGenes_UCSC, transcript_ENSEMBL,

Examples

# Oboselet function

library("Gviz")
library("rtracklayer")
gen <- "hg19"
chr <- "chr2"
start <- 38292433
end <- 38305492

if(interactive()){
  BROWSER.SESSION="UCSC"
  mySession <- browserSession(BROWSER.SESSION)
  genome(mySession) <- gen
  iscatrack <-ISCA_UCSC(gen,chrom,start,end,mySession,title="ISCA", table="iscaPathogenic")
  plotTracks(iscatrack, from = start, to =end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(ISCAtrack_Grch38)
  plotTracks(iscatrack, from = start, to =end,
                                   fontfamily="sans",fontfamily.title="sans")
}

Description

Create a track of known genes from the UCSC genome browser using the Gviz bioconductor package

Usage

knownGenes_UCSC(gen, chr, start, end,title="UCSC known Genes", showId=TRUE)

Arguments

Value

An UcscTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=knownGene

http://bioconductor.org/packages/release/bioc/html/Gviz.html

See Also

ISCA_UCSC, GWAScatalog_UCSC, genesName_ENSEMBL, GeneReviews_UCSC, GAD_UCSC, genes_ENSEMBL, xenorefGenes_UCSC, transcript_ENSEMBL,

Examples

library("Gviz")
gen <- "hg38"
chr <- "chr7"
start <- 38290160
end <- 38303219

if(interactive()) {
  genesUcsctrack<-knownGenes_UCSC(gen,chr,start,end,showId=TRUE)
  plotTracks(genesUcsctrack, from = start, to =end,
                                   fontfamily="sans",fontfamily.title="sans")
}else {
  data(genesUcsctrack)
  plotTracks(genesUcsctrack, from = start, to =end,
                                   fontfamily="sans",fontfamily.title="sans")
}

Description

Creates a track from a BED file for metQTL data using the Gviz bioconductor package. A complete list of features and their associated colours can be found in the user guide.

Usage

metQTL(gen, chr, start, end, bedFilePath, featureDisplay, showId=FALSE,
type_stacking="squish",just_group="above", title="metQTL")

Arguments

Value

An AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

Tom Hardiman

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

Got to ENSEMBLregulation binding motif biomart

Examples

library("Gviz")

gen <- 'hg19'
chr <- "chr15"
start <- 74889136
end <-   75018200
featureDisplay <- "trans_local_metQTL"
type_stacking <- "squish"

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
mqtlbedFilePath <- file.path(extdata, "metQTL.bed")

if(interactive()){
  metQTLTrackSingle <- metQTL(gen,chr,start, end,mqtlbedFilePath,
  featureDisplay = featureDisplay )
  plotTracks(metQTLTrackSingle, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(metQTLTrackSingle)
  plotTracks(metQTLTrackSingle, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
}

###

library("Gviz")

gen <- 'hg19'
chr <- "chr15"
start <- 74889136
end <-   75018200

featureDisplay <- c("trans_local_metQTL","CpG")

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
bedFilePath <- file.path(extdata, "metQTL.bed")

if(interactive()){
  metQTLTrackMultiple <- metQTL(gen,chr,start, end, bedFilePath,
  featureDisplay = featureDisplay )
  plotTracks(metQTLTrackMultiple, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(metQTLTrackMultiple)
  plotTracks(metQTLTrackMultiple, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
}

#####

library("Gviz")

gen <- 'hg19'
chr <- "chr15"
start <- 74889136
end <-   75018200

featureDisplay <- "all"

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
bedFilePath <- file.path(extdata, "metQTL.bed")

if(interactive()){
  metQTLTrackAll <- metQTL(gen,chr,start, end, bedFilePath,
  featureDisplay = featureDisplay )
  plotTracks(metQTLTrackAll, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(metQTLTrackAll)
  plotTracks(metQTLTrackAll, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
}

Description

Creates a track of miRNA target regions from ENSEMBL using the Gviz bioconductor package.

Usage

miRNATargetRegionsBiomart_ENSEMBL(gen, chr, start, end, showId=FALSE,
datasetEnsembl = "hsapiens_mirna_target_feature",
title="miRNA Target Regions ENSEMBL")

Arguments

Value

An AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

Tom Hardiman

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

Got to ENSEMBLregulation binding motif biomart

Examples

library("Gviz")
gen <- "hg38"
chr <- "chr1"
start <- 1000000
end <- 20000000


if(interactive()){
 miRNATargetRegionsBiomartTrack<-miRNATargetRegionsBiomart_ENSEMBL(gen,chr,start,end,
                                      datasetEnsembl = "hsapiens_mirna_target_feature")
  plotTracks(miRNATargetRegionsBiomartTrack, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(miRNATargetRegionsBiomartTrack)
  plotTracks(miRNATargetRegionsBiomartTrack, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
}

Description

Creates a track from ENSEMBL of other regulatory regions using the Gviz bioconductor package. A complete list of features and their associated colours can be found in the user guide.

Usage

otherRegulatoryRegionsBiomart_ENSEMBL(gen, chr, start, end,
featureDisplay = "all",datasetEnsembl = "hsapiens_external_feature",
title="Other Regulatory Regions ENSEMBL")

Arguments

Value

An AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

Tom Hardiman

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

Got to ENSEMBLregulation binding motif biomart

Examples

library("Gviz")
gen <- "hg38"
chr <- "chr1"
start <- 100000
end <- 5000000
featureDisplay <- "Enhancer"

if(interactive()){
 otherRegulatoryRegionsTrackSingle<-otherRegulatoryRegionsBiomart_ENSEMBL(gen,
 chr,start,end,featureDisplay)
  plotTracks(otherRegulatoryRegionsTrackSingle, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(otherRegulatoryRegionsTrackSingle)
  plotTracks(otherRegulatoryRegionsTrackSingle, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
}

########

library("Gviz")
gen <- "hg38"
chr <- "chr1"
start <- 100000
end <- 5000000
featureDisplay <- "all"

if(interactive()){
 otherRegulatoryRegionsTrackAll<-otherRegulatoryRegionsBiomart_ENSEMBL(gen,
 chr,start,end,featureDisplay)
  plotTracks(otherRegulatoryRegionsTrackAll, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(otherRegulatoryRegionsTrackAll)
  plotTracks(otherRegulatoryRegionsTrackAll, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")

}

Description

This function displays a color wheel with specified colors

Usage

pizza(colors, bg = "gray95", border = NA,
    init.angle = 105, cex = 0.8, lty = 1, labcol = NULL,
    ...)

Arguments

Details

This function is based on the pie function

Author(s)

Gaston Sanchez

Examples

# pizza color wheel for rainbow colors
pizza(rainbow(7))

# pizza color wheel for tomato (18 colors)
pizza(setColors("tomato", 18), bg = "gray20", cex = 0.7)

Description

Creates a track of psiQTL from GTEx using the Gviz bioconductor package. A complete list of features and their associated colours can be found in the user guide.

Usage

psiQTL_GTEx(gen,chr,start, end, bedFilePath, featureDisplay = 'all',
showId=FALSE, type_stacking="squish",just_group="above", title="psiQTL GTEX")

Arguments

Value

An AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

Got to BindingMotifsBiomart binding motif biomart

Examples

library("Gviz")
gen <- "hg19"
chr<-"chr13"
start <- 52713837
end <- 52715894
extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
psiQTLFilePath <- file.path(extdata, "/GTEX/psiQTL_Assoc-total.AdiposeTissue.txt")


if(interactive()){
  psiGTexTrackall<- psiQTL_GTEx(gen,chr,start, end, psiQTLFilePath,
  featureDisplay = 'all', showId=TRUE, type_stacking="squish",
  just_group="above" )
  plotTracks(psiGTexTrackall, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(psiGTexTrackall)
  plotTracks(psiGTexTrackall, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
}

if(interactive()){
 psiGTexTrackSNP<- psiQTL_GTEx(gen,chr,start, end, psiQTLFilePath,
 featureDisplay = 'SNP', showId=TRUE, type_stacking="squish",
 just_group="left")
  plotTracks(psiGTexTrackSNP, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(psiGTexTrackSNP)
  plotTracks(psiGTexTrackSNP, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
}

Description

Create a track of RefSeq genes from the UCSC genome browser using the Gviz bioconductor package

Usage

refGenes_UCSC(gen, chr, start, end, title="Ref Genes UCSC", track = "refGene",
IdType="Ref", showId=TRUE)