Package 'Site2Target' reference manual

Title:	An R package to associate peaks and target genes
Description:	Statistics implemented for both peak-wise and gene-wise associations. In peak-wise associations, the p-value of the target genes of a given set of peaks are calculated. Negative binomial or Poisson distributions can be used for modeling the unweighted peaks targets and log-nromal can be used to model the weighted peaks. In gene-wise associations a table consisting of a set of genes, mapped to specific peaks, is generated using the given rules.
Authors:	Peyman Zarrineh [cre, aut] (ORCID: <https://orcid.org/0000-0003-4820-4101>)
Maintainer:	Peyman Zarrineh <[email protected]>
License:	GPL-2
Version:	1.5.0
Built:	2026-05-23 09:43:56 UTC
Source:	https://github.com/bioc/Site2Target

Add column to gene-wise association

Description

Add a column of values based on the type either genes or peaks.

The Input is either coordinates or names of genes or peaks plus

a column of relevant values. This function add these values as

a column to gene or peak table as well as the interaction table.

Usage

addColumn2geneWiseAssociation(
  type = "",
  name = NULL,
  coordinates = NULL,
  columnName = NA,
  column,
  inFile = "geneWiseAssociation",
  outFile = "geneWiseAssociation"
)
addColumn2geneWiseAssociation(
  type = "",
  name = NULL,
  coordinates = NULL,
  columnName = NA,
  column,
  inFile = "geneWiseAssociation",
  outFile = "geneWiseAssociation"
)

Arguments

type

type of columns to be added. Either "gene" or "peak"

name

Names of genes or peaks

coordinates

Coordinates of genes or peaks in granges format

columnName

Column name that should be added to the tables

column

Column values that should be added to the tables

inFile

The name of the input folder (default "genewiseAssociation")

outFile

The name of the output folder (default "genewiseAssociation")

Value

No value returns just column would be added to the tables

Examples

geneFile=system.file("extdata", "gene_expression.tsv", package="Site2Target")
geneCoords <- Table2Granges(geneFile)
geneTable <- read.table(geneFile, header=TRUE)

geneDEIndices <- which((abs(geneTable$logFC)>1)==TRUE)
indicesLen <- length(geneDEIndices)
if(indicesLen >0)
{
    geneTable <- geneTable[geneDEIndices,]
    geneCoords <- geneCoords[geneDEIndices]
}
geneDENames <- geneTable$name
geneDElogFC <- geneTable$logFC
geneCoordsDE <- geneCoords

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)
tfTable <- read.table(tfFile, header=TRUE)
tfIntensities <- tfTable$intensities

stats <-
genewiseAssociation(associationBy="distance",
                    geneCoordinates=geneCoordsDE,
                    geneNames=geneDENames,
                    peakCoordinates=TFCoords,
                    distance=50000,
                    outFile="Gene_TF_50K")
stats

# add expression log fold changes to the table
addColumn2geneWiseAssociation(type="gene", name=geneDENames,
   columnName="Expr_logFC", column=geneDElogFC, inFile="Gene_TF_50K",
   outFile="Gene_TF_50K")

# add peak intensitites to the table
addColumn2geneWiseAssociation(type="peak", coordinates=TFCoords,
   columnName="Binding_Intensities", column=tfIntensities,
   inFile="Gene_TF_50K", outFile="Gene_TF_50K")
geneFile=system.file("extdata", "gene_expression.tsv", package="Site2Target")
geneCoords <- Table2Granges(geneFile)
geneTable <- read.table(geneFile, header=TRUE)

geneDEIndices <- which((abs(geneTable$logFC)>1)==TRUE)
indicesLen <- length(geneDEIndices)
if(indicesLen >0)
{
    geneTable <- geneTable[geneDEIndices,]
    geneCoords <- geneCoords[geneDEIndices]
}
geneDENames <- geneTable$name
geneDElogFC <- geneTable$logFC
geneCoordsDE <- geneCoords

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)
tfTable <- read.table(tfFile, header=TRUE)
tfIntensities <- tfTable$intensities

stats <-
genewiseAssociation(associationBy="distance",
                    geneCoordinates=geneCoordsDE,
                    geneNames=geneDENames,
                    peakCoordinates=TFCoords,
                    distance=50000,
                    outFile="Gene_TF_50K")
stats

# add expression log fold changes to the table
addColumn2geneWiseAssociation(type="gene", name=geneDENames,
   columnName="Expr_logFC", column=geneDElogFC, inFile="Gene_TF_50K",
   outFile="Gene_TF_50K")

# add peak intensitites to the table
addColumn2geneWiseAssociation(type="peak", coordinates=TFCoords,
   columnName="Binding_Intensities", column=tfIntensities,
   inFile="Gene_TF_50K", outFile="Gene_TF_50K")

Add a relation column to gene-peak interaction table

Description

Get coordinates of interactions (ex. HiC interactions) and a

column of interaction values (ex. HiC intensities ) and add them

as a column to gene-peak interaction table.

Usage

addRelation2geneWiseAssociation(
  strand1 = NULL,
  strand2 = NULL,
  columnName,
  column,
  inFile = "geneWiseAssociation",
  outFile = "geneWiseAssociation"
)
addRelation2geneWiseAssociation(
  strand1 = NULL,
  strand2 = NULL,
  columnName,
  column,
  inFile = "geneWiseAssociation",
  outFile = "geneWiseAssociation"
)

Arguments

strand1

granges of DNA strand1 linked to DNA strand2

strand2

granges of DNA strand2 linked to DNA strand1

columnName

Column name that should be added to the interaction table

column

Column values that should be added to the interaction table

inFile

The name of the input folder (default "genewiseAssociation")

outFile

The name of the output folder (default "genewiseAssociation")

Value

No value would be returned just a column be added to link table

Examples

geneFile=system.file("extdata", "gene_expression.tsv", package="Site2Target")
geneCoords <- Table2Granges(geneFile)
geneTable <- read.table(geneFile, header=TRUE)

geneDEIndices <- which((abs(geneTable$logFC)>1)==TRUE)
indicesLen <- length(geneDEIndices)
if(indicesLen >0)
{
    geneTable <- geneTable[geneDEIndices,]
    geneCoords <- geneCoords[geneDEIndices]
}
geneDENames <- geneTable$name
geneDElogFC <- geneTable$logFC
geneCoordsDE <- geneCoords

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)
tfTable <- read.table(tfFile, header=TRUE)

stats <-
genewiseAssociation(associationBy="distance",
                    geneCoordinates=geneCoordsDE,
                    geneNames=geneDENames,
                    peakCoordinates=TFCoords,
                    distance=50000,
                    outFile="Gene_TF_50K")
stats

HiCFile =system.file("extdata", "HiC_intensities.tsv", package="Site2Target")
HiCstr1 <- Table2Granges(HiCFile, chrColName="Strand1_chr",
                     startColName="Strand1_start", endColName="Strand1_end")
HiCstr2 <- Table2Granges(HiCFile, chrColName="Strand2_chr",
                     startColName="Strand2_start", endColName="Strand2_end")
HiCTable <- read.table(HiCFile, header=TRUE)
HiCintensities <- HiCTable$intensities

addRelation2geneWiseAssociation(strand1=HiCstr1, strand2=HiCstr2,
     columnName="HiC_Intensities", column=HiCintensities,
     inFile="Gene_TF_50K", outFile="Gene_TF_50K")
geneFile=system.file("extdata", "gene_expression.tsv", package="Site2Target")
geneCoords <- Table2Granges(geneFile)
geneTable <- read.table(geneFile, header=TRUE)

geneDEIndices <- which((abs(geneTable$logFC)>1)==TRUE)
indicesLen <- length(geneDEIndices)
if(indicesLen >0)
{
    geneTable <- geneTable[geneDEIndices,]
    geneCoords <- geneCoords[geneDEIndices]
}
geneDENames <- geneTable$name
geneDElogFC <- geneTable$logFC
geneCoordsDE <- geneCoords

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)
tfTable <- read.table(tfFile, header=TRUE)

stats <-
genewiseAssociation(associationBy="distance",
                    geneCoordinates=geneCoordsDE,
                    geneNames=geneDENames,
                    peakCoordinates=TFCoords,
                    distance=50000,
                    outFile="Gene_TF_50K")
stats

HiCFile =system.file("extdata", "HiC_intensities.tsv", package="Site2Target")
HiCstr1 <- Table2Granges(HiCFile, chrColName="Strand1_chr",
                     startColName="Strand1_start", endColName="Strand1_end")
HiCstr2 <- Table2Granges(HiCFile, chrColName="Strand2_chr",
                     startColName="Strand2_start", endColName="Strand2_end")
HiCTable <- read.table(HiCFile, header=TRUE)
HiCintensities <- HiCTable$intensities

addRelation2geneWiseAssociation(strand1=HiCstr1, strand2=HiCstr2,
     columnName="HiC_Intensities", column=HiCintensities,
     inFile="Gene_TF_50K", outFile="Gene_TF_50K")

MEIS cardiomyocytes datasets used in the package

Description

Human cardiomyocytes datasets are reduced in size by only using chr21. log fold changes of Gene expression WT vs MEIS KO from RNA-seq experiments, and binding sites of MEIS derived from a ChIP-seq experiment are the main experimental datasets representing relevant gene and peak information. HiC interactions and topologically associating domains (TADs) are derived from a HiC experiments are auxiliary datasets related to DNA-DNA interactions.

Format

Gene expression WT vs MEIS KO in chr21. MEIS binding sites in chr21. TADs, and HiC interactions in chr21.

gene_expression.tsv: Gene expression
MEIS_binding.tsv: MEIS binding sites
TADs.tsv: TADs
HiC_intensities.tsv: HiC interactions

Value

Just description of data

Examples


## Gene expression table

# Read gene coordinates 
geneFile=system.file("extdata", "gene_expression.tsv",
                     package="Site2Target")
geneCoords <- Table2Granges(geneFile)

# Read gene table
geneTable <- read.table(geneFile, header=TRUE)



## TF binding table

# Read peak coordinates
tfFile =system.file("extdata", "MEIS_binding.tsv",
                    package="Site2Target")
TFCoords <- Table2Granges(tfFile)

# Read MEIS binding intensities
tfTable <- read.table(tfFile, header=TRUE)


## DNA-DNA interactions

# Read TAD regions
TADsFile =system.file("extdata", "TADs.tsv",
                               package="Site2Target")
TADs <- Table2Granges(TADsFile)


# Read HiC interactions
HiCFile =system.file("extdata", "HiC_intensities.tsv",
                               package="Site2Target")
HiCstr1 <- Table2Granges(HiCFile, chrColName="Strand1_chr",
                      startColName="Strand1_start", endColName="Strand1_end")
HiCstr2 <- Table2Granges(HiCFile, chrColName="Strand2_chr",
                     startColName="Strand2_start", endColName="Strand2_end")

HiCTable <- read.table(HiCFile, header=TRUE)


## Gene expression table

# Read gene coordinates 
geneFile=system.file("extdata", "gene_expression.tsv",
                     package="Site2Target")
geneCoords <- Table2Granges(geneFile)

# Read gene table
geneTable <- read.table(geneFile, header=TRUE)



## TF binding table

# Read peak coordinates
tfFile =system.file("extdata", "MEIS_binding.tsv",
                    package="Site2Target")
TFCoords <- Table2Granges(tfFile)

# Read MEIS binding intensities
tfTable <- read.table(tfFile, header=TRUE)


## DNA-DNA interactions

# Read TAD regions
TADsFile =system.file("extdata", "TADs.tsv",
                               package="Site2Target")
TADs <- Table2Granges(TADsFile)


# Read HiC interactions
HiCFile =system.file("extdata", "HiC_intensities.tsv",
                               package="Site2Target")
HiCstr1 <- Table2Granges(HiCFile, chrColName="Strand1_chr",
                      startColName="Strand1_start", endColName="Strand1_end")
HiCstr2 <- Table2Granges(HiCFile, chrColName="Strand2_chr",
                     startColName="Strand2_start", endColName="Strand2_end")

HiCTable <- read.table(HiCFile, header=TRUE)

Extend sites given regions boundaries

Description

Get sites and given regions (ex. TADs or loops) coordinates.

It extends sites in a give region using a distance function

Usage

extendSitesInGivenRegions(givenRegions, sites, distance = 1e+05)
extendSitesInGivenRegions(givenRegions, sites, distance = 1e+05)

Arguments

givenRegions

granges coordinates of given regions (ex. TAD or loops)

sites

granges coordinates of sites

distance

the maximum distance to associate sites to regions

Value

A granges of the extended sites in given regions

Examples

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)

TADsFile =system.file("extdata", "TADs.tsv",package="Site2Target")
TADs <- Table2Granges(TADsFile)

extendSitesInGivenRegions(TADs, TFCoords)

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)

TADsFile =system.file("extdata", "TADs.tsv",package="Site2Target")
TADs <- Table2Granges(TADsFile)

extendSitesInGivenRegions(TADs, TFCoords)

Generate genewise association between genes and peaks

Description

Get genomic coordinates of a set of genes and a set of peaks

associate them by a fixed distance (default 50K nt). It also

associate genes and peaks for provided DNA-DNA interaction from

a dataset like HiC. This function can also associate genes and

user provided regions (ex. TADs, subTADs, etc). It generates

three tables: Gene table, peak table, and Gene-Peak association

table.

Usage

genewiseAssociation(
  associationBy = "distance",
  geneCoordinates = NULL,
  geneNames = NULL,
  peakCoordinates = NULL,
  peakNames = NULL,
  distance = 50000,
  givenRegions = NULL,
  strand1 = NULL,
  strand2 = NULL,
  outFile = "genewiseAssociation"
)
genewiseAssociation(
  associationBy = "distance",
  geneCoordinates = NULL,
  geneNames = NULL,
  peakCoordinates = NULL,
  peakNames = NULL,
  distance = 50000,
  givenRegions = NULL,
  strand1 = NULL,
  strand2 = NULL,
  outFile = "genewiseAssociation"
)

Arguments

associationBy

Can be "distance", "regions", or "DNAinteractions"

geneCoordinates

Gene coordinates in granges format

geneNames

Gene names can be provided by the user

peakCoordinates

Peak coordinates in granges format

peakNames

Peak names can be provided by the user

distance

The maximum distance to associate peaks to genes. default 50K

givenRegions

granges coordinates of given regions (ex. TAD or loops)

strand1

granges of DNA strand1 linked to DNA strand2

strand2

granges of DNA strand2 linked to DNA strand1

outFile

The name of the output folder (default "genewiseAssociation")

Value

A vector of portions of linked genes and linked peaks

Examples

geneFile=system.file("extdata", "gene_expression.tsv", package="Site2Target")
geneCoords <- Table2Granges(geneFile)
geneTable <- read.table(geneFile, header=TRUE)

geneDEIndices <- which((abs(geneTable$logFC)>1)==TRUE)
indicesLen <- length(geneDEIndices)
if(indicesLen >0)
{
    geneTable <- geneTable[geneDEIndices,]
    geneCoords <- geneCoords[geneDEIndices]
}
geneDENames <- geneTable$name
geneDElogFC <- geneTable$logFC
geneCoordsDE <- geneCoords

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)
tfTable <- read.table(tfFile, header=TRUE)

stats <-
genewiseAssociation(associationBy="distance",
                    geneCoordinates=geneCoordsDE,
                    geneNames=geneDENames,
                    peakCoordinates=TFCoords,
                    distance=50000,
                    outFile="Gene_TF_50K")
stats
geneFile=system.file("extdata", "gene_expression.tsv", package="Site2Target")
geneCoords <- Table2Granges(geneFile)
geneTable <- read.table(geneFile, header=TRUE)

geneDEIndices <- which((abs(geneTable$logFC)>1)==TRUE)
indicesLen <- length(geneDEIndices)
if(indicesLen >0)
{
    geneTable <- geneTable[geneDEIndices,]
    geneCoords <- geneCoords[geneDEIndices]
}
geneDENames <- geneTable$name
geneDElogFC <- geneTable$logFC
geneCoordsDE <- geneCoords

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)
tfTable <- read.table(tfFile, header=TRUE)

stats <-
genewiseAssociation(associationBy="distance",
                    geneCoordinates=geneCoordsDE,
                    geneNames=geneDENames,
                    peakCoordinates=TFCoords,
                    distance=50000,
                    outFile="Gene_TF_50K")
stats

Return center of the given granges files

Description

Get a granges and find the center of it

Usage

getCenterOfPeaks(gr)
getCenterOfPeaks(gr)

Arguments

gr

granges coordinate

Value

granges format of the center

Examples

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)
TFCoordsCenters <- getCenterOfPeaks(TFCoords)
TFCoordsCenters

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)
TFCoordsCenters <- getCenterOfPeaks(TFCoords)
TFCoordsCenters

Get names of genes or peaks related to a query coordinates

Description

Get names and coordinates of genes or peaks. It also get the

coordinates of query regions and returns the related genes or

peak names.

Usage

getNameFromCoordinates(names, coordinates, queryCoordinates)
getNameFromCoordinates(names, coordinates, queryCoordinates)

Arguments

names

Names of genes or peaks

coordinates

Coordinates of genes or peaks in granges format

queryCoordinates

Coordinates of the query regions in granges format

Value

Names of genes or peaks in queried regions

generate number of sites per gene given distances

Description

Get genes and sites coordinates, and associate them by given

distance.

Usage

getTargetGenesNumber(geneCoordinates = NA, sites = NA, distance = 50000)
getTargetGenesNumber(geneCoordinates = NA, sites = NA, distance = 50000)

Arguments

geneCoordinates

granges coordinates of genes

sites

granges coordinates of sites

distance

the maximum distance to associate sites to genes. default 50K

Value

A vector sites number matched to each gene

Examples

geneFile=system.file("extdata", "gene_expression.tsv", package="Site2Target")
geneCoords <- Table2Granges(geneFile)

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)

targetNum <- getTargetGenesNumber( geneCoords, TFCoords)

geneFile=system.file("extdata", "gene_expression.tsv", package="Site2Target")
geneCoords <- Table2Granges(geneFile)

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)

targetNum <- getTargetGenesNumber( geneCoords, TFCoords)

Fit Negative binomial distribution to target genes

Description

Get genes and sites coordinates, and associate them by given

distance or given regions (ex. TADs or loops). It tests the

distribution of sites around genes either by poisson or

negative binomial test.

Usage

getTargetGenesPvals(
  associationBy = "distance",
  dist = "negative binomial",
  geneCoordinates = NA,
  sites = NA,
  distance = 50000,
  givenRegions = NA
)
getTargetGenesPvals(
  associationBy = "distance",
  dist = "negative binomial",
  geneCoordinates = NA,
  sites = NA,
  distance = 50000,
  givenRegions = NA
)

Arguments

associationBy

either "distance" or "regions"

dist

either "negative binomial" or "poisson"

geneCoordinates

granges coordinates of genes

sites

granges coordinates of sites

distance

the maximum distance to associate sites to genes. default 50K

givenRegions

user provided granges regions like TADs or loops

Value

A vector of pvalue distribution for target genes

Examples


geneFile=system.file("extdata", "gene_expression.tsv", package="Site2Target")
geneCoords <- Table2Granges(geneFile)

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)

pvals <- getTargetGenesPvals( geneCoordinates=geneCoords, sites=TFCoords)

geneFile=system.file("extdata", "gene_expression.tsv", package="Site2Target")
geneCoords <- Table2Granges(geneFile)

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)

pvals <- getTargetGenesPvals( geneCoordinates=geneCoords, sites=TFCoords)

Fit Negative binomial distribution to target genes

Description

Get genes and sites coordinates, and associate them by given

distance and user provided DNA interaction (ex. HiC). It tests

the distribution of sites around genes either by poisson or

negative binomial test.

Usage

getTargetGenesPvalsWithDNAInteractions(
  dist = "negative binomial",
  geneCoordinates = NA,
  sites = NA,
  strand1 = NA,
  strand2 = NA,
  distance = 50000
)
getTargetGenesPvalsWithDNAInteractions(
  dist = "negative binomial",
  geneCoordinates = NA,
  sites = NA,
  strand1 = NA,
  strand2 = NA,
  distance = 50000
)

Arguments

dist

either "negative binomial" or "poisson"

geneCoordinates

granges coordinates of genes

sites

granges coordinates of sites

strand1

granges of DNA strand1 linked to DNA strand2

strand2

granges of DNA strand2 linked to DNA strand1

distance

the maximum distance to associate sites to genes. default 50K

Value

A vector of pvalue distribution for target genes

Examples


geneFile=system.file("extdata", "gene_expression.tsv", package="Site2Target")
geneCoords <- Table2Granges(geneFile)

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)

HiCFile =system.file("extdata", "HiC_intensities.tsv", package="Site2Target")
HiCstr1 <- Table2Granges(HiCFile, chrColName="Strand1_chr",
                     startColName="Strand1_start", endColName="Strand1_end")
HiCstr2 <- Table2Granges(HiCFile, chrColName="Strand2_chr",
                     startColName="Strand2_start", endColName="Strand2_end")

pvals <- getTargetGenesPvalsWithDNAInteractions(
               geneCoordinates=geneCoords, sites=TFCoords, strand1=HiCstr1,
               strand2=HiCstr2)

geneFile=system.file("extdata", "gene_expression.tsv", package="Site2Target")
geneCoords <- Table2Granges(geneFile)

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)

HiCFile =system.file("extdata", "HiC_intensities.tsv", package="Site2Target")
HiCstr1 <- Table2Granges(HiCFile, chrColName="Strand1_chr",
                     startColName="Strand1_start", endColName="Strand1_end")
HiCstr2 <- Table2Granges(HiCFile, chrColName="Strand2_chr",
                     startColName="Strand2_start", endColName="Strand2_end")

pvals <- getTargetGenesPvalsWithDNAInteractions(
               geneCoordinates=geneCoords, sites=TFCoords, strand1=HiCstr1,
               strand2=HiCstr2)

Fit log-normal distribution to target genes

Description

Get genes and sites coordinates, and associate them by given

distance or given regions (ex. TADs or loops). It tests the

distribution of log-intensities of sites around genes by

log-normal test. This function consider both binding sites and

intensities.

Usage

getTargetGenesPvalsWithIntensities(
  associationBy = "distance",
  intensities,
  geneCoordinates = NA,
  sites = NA,
  distance = 50000,
  givenRegions = NA
)
getTargetGenesPvalsWithIntensities(
  associationBy = "distance",
  intensities,
  geneCoordinates = NA,
  sites = NA,
  distance = 50000,
  givenRegions = NA
)

Arguments

associationBy

either "distance" or "regions"

intensities

intensity values associated to sites

geneCoordinates

granges coordinates of genes

sites

granges coordinates of sites

distance

the maximum distance to associate sites to genes. default 50K

givenRegions

user provided granges regions like TADs or loops

Value

A vector of pvalue distribution for target genes

Examples


geneFile=system.file("extdata", "gene_expression.tsv", package="Site2Target")
geneCoords <- Table2Granges(geneFile)

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)
tfTable <- read.table(tfFile, header=TRUE)
tfIntensities <- tfTable$intensities

pvals <- getTargetGenesPvalsWithIntensities(geneCoordinates=geneCoords,
                      sites=TFCoords, intensities=tfIntensities)

geneFile=system.file("extdata", "gene_expression.tsv", package="Site2Target")
geneCoords <- Table2Granges(geneFile)

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)
tfTable <- read.table(tfFile, header=TRUE)
tfIntensities <- tfTable$intensities

pvals <- getTargetGenesPvalsWithIntensities(geneCoordinates=geneCoords,
                      sites=TFCoords, intensities=tfIntensities)

Fit log-normal distribution to target genes

Description

Get genes and sites coordinates, and associate them by given

distance and user provided DNA interaction (ex. HiC). It tests

the distribution of log-intensities of sites around genes by

log-normal test. This function consider both binding sites and

intensities.

Usage

getTargetGenesPvalsWithIntensitiesAndDNAInteractions(
  geneCoordinates,
  sites,
  intensities,
  strand1,
  strand2,
  distance = 50000
)
getTargetGenesPvalsWithIntensitiesAndDNAInteractions(
  geneCoordinates,
  sites,
  intensities,
  strand1,
  strand2,
  distance = 50000
)

Arguments

geneCoordinates

granges coordinates of genes

sites

granges coordinates of sites

intensities

intensity values associated to sites

strand1

granges of DNA strand1 linked to DNA strand2

strand2

granges of DNA strand2 linked to DNA strand1

distance

the maximum distance to associate sites to genes. default 50K

Value

A vector of pvalue distribution for target genes

Examples


geneFile=system.file("extdata", "gene_expression.tsv", package="Site2Target")
geneCoords <- Table2Granges(geneFile)

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)
tfTable <- read.table(tfFile, header=TRUE)
tfIntensities <- tfTable$intensities

HiCFile =system.file("extdata", "HiC_intensities.tsv", package="Site2Target")
HiCstr1 <- Table2Granges(HiCFile, chrColName="Strand1_chr",
                     startColName="Strand1_start", endColName="Strand1_end")
HiCstr2 <- Table2Granges(HiCFile, chrColName="Strand2_chr",
                     startColName="Strand2_start", endColName="Strand2_end")

pvals <- getTargetGenesPvalsWithIntensitiesAndDNAInteractions(
                       geneCoordinates=geneCoords, sites=TFCoords,
                       intensities=tfIntensities, strand1=HiCstr1,
                        strand2=HiCstr2)

geneFile=system.file("extdata", "gene_expression.tsv", package="Site2Target")
geneCoords <- Table2Granges(geneFile)

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)
tfTable <- read.table(tfFile, header=TRUE)
tfIntensities <- tfTable$intensities

HiCFile =system.file("extdata", "HiC_intensities.tsv", package="Site2Target")
HiCstr1 <- Table2Granges(HiCFile, chrColName="Strand1_chr",
                     startColName="Strand1_start", endColName="Strand1_end")
HiCstr2 <- Table2Granges(HiCFile, chrColName="Strand2_chr",
                     startColName="Strand2_start", endColName="Strand2_end")

pvals <- getTargetGenesPvalsWithIntensitiesAndDNAInteractions(
                       geneCoordinates=geneCoords, sites=TFCoords,
                       intensities=tfIntensities, strand1=HiCstr1,
                        strand2=HiCstr2)

Convert granges to strings of coordinates

Description

Get genomic coordinates granges and convert them to strings

Usage

granges2String(gr)
granges2String(gr)

Arguments

gr

granges coordinates

Value

string of coordinates

Examples

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)
strCoords <- granges2String(TFCoords)
head(strCoords)

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)
strCoords <- granges2String(TFCoords)
head(strCoords)

Remove reserved characters from a string

Description

Remove reserved characters (such as *, +, -, etc) from a string

Usage

removeReserveCharacter(name)
removeReserveCharacter(name)

Arguments

name

A string of characters

Value

A string without reserved characters

Examples

removeReserveCharacter("A&%B^f6")

removeReserveCharacter("A&%B^f6")

Return the distance between paired peaks and genes

Description

Get a granges of genes and peaks and return their distances

Usage

site2GeneDistance(geneCoordinates, peakCoordinates)
site2GeneDistance(geneCoordinates, peakCoordinates)

Arguments

geneCoordinates

granges coordinates of genes

peakCoordinates

granges coordinates of peaks

Value

the respective distances of paired genes and peaks

Associate peaks and target genes

Description

Statistical implementation for both peak-wise and gene-wise associations. Here is an example of a peak-wise and a gene-wise association of differential genes WT vs KO of a transcription factor and binding sites of this transcription factor.

Value

Just an example

Examples

geneFile=system.file("extdata", "gene_expression.tsv", package="Site2Target")
geneCoords <- Table2Granges(geneFile)
geneTable <- read.table(geneFile, header=TRUE)

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)
tfTable <- read.table(tfFile, header=TRUE)

## Peakwise association example

pvals <- getTargetGenesPvals(geneCoordinates=geneCoords, sites=TFCoords)
topTargetNum <- 5
topTargetIndex <- order(pvals)[1:topTargetNum]

# Make a data frame of peak targets pvalues and expression logFCs

dfTopTarget <- 
  data.frame(name=geneTable$name[topTargetIndex],
             pvalue=pvals[topTargetIndex],
             exprLogC=geneTable$logFC[topTargetIndex]
             )
dfTopTarget

## Genewise association example
geneDEIndices <- which((abs(geneTable$logFC)>1)==TRUE)
indicesLen <- length(geneDEIndices)
if(indicesLen >0)
{
    geneTable <- geneTable[geneDEIndices,]
    geneCoords <- geneCoords[geneDEIndices]
}
geneDENames <- geneTable$name
geneDElogFC <- geneTable$logFC
geneCoordsDE <- geneCoords

stats <-
genewiseAssociation(associationBy="distance",
                    geneCoordinates=geneCoordsDE,
                    geneNames=geneDENames,
                    peakCoordinates=TFCoords,
                    distance=50000,
                    outFile="Gene_TF_50K")
stats
geneFile=system.file("extdata", "gene_expression.tsv", package="Site2Target")
geneCoords <- Table2Granges(geneFile)
geneTable <- read.table(geneFile, header=TRUE)

tfFile =system.file("extdata", "MEIS_binding.tsv", package="Site2Target")
TFCoords <- Table2Granges(tfFile)
tfTable <- read.table(tfFile, header=TRUE)

## Peakwise association example

pvals <- getTargetGenesPvals(geneCoordinates=geneCoords, sites=TFCoords)
topTargetNum <- 5
topTargetIndex <- order(pvals)[1:topTargetNum]

# Make a data frame of peak targets pvalues and expression logFCs

dfTopTarget <- 
  data.frame(name=geneTable$name[topTargetIndex],
             pvalue=pvals[topTargetIndex],
             exprLogC=geneTable$logFC[topTargetIndex]
             )
dfTopTarget

## Genewise association example
geneDEIndices <- which((abs(geneTable$logFC)>1)==TRUE)
indicesLen <- length(geneDEIndices)
if(indicesLen >0)
{
    geneTable <- geneTable[geneDEIndices,]
    geneCoords <- geneCoords[geneDEIndices]
}
geneDENames <- geneTable$name
geneDElogFC <- geneTable$logFC
geneCoordsDE <- geneCoords

stats <-
genewiseAssociation(associationBy="distance",
                    geneCoordinates=geneCoordsDE,
                    geneNames=geneDENames,
                    peakCoordinates=TFCoords,
                    distance=50000,
                    outFile="Gene_TF_50K")
stats

Convert strings to granges of coordinates

Description

Get genomic coordinates as strings and convert them to granges

Usage

string2Granges(strCoordinates)
string2Granges(strCoordinates)

Arguments

strCoordinates

string of coordinates

Value

Genomic coordinates in granges format

Examples

string2Granges(c("chr1:1112-1231", "ch2:3131-3221"))

string2Granges(c("chr1:1112-1231", "ch2:3131-3221"))

Take Genomic Ranges from a table file

Description

Read a table file and derive genomic ranges from user provided

column names.

Usage

Table2Granges(
  fileName,
  chrColName = "chr",
  startColName = "start",
  endColName = "end"
)
Table2Granges(
  fileName,
  chrColName = "chr",
  startColName = "start",
  endColName = "end"
)

Arguments

fileName

A table delimited file

chrColName

Chromosomes column name (default: "Chr")

startColName

Start column name (default: "start")

endColName

End column name (default: "end")

Value

granges format of given coordinates

Examples


geneFile=system.file("extdata", "gene_expression.tsv", package="Site2Target")
grs <- Table2Granges(fileName=geneFile,
                      chrColName="chr",
                       startColName="start",
                       endColName="end")
grs

geneFile=system.file("extdata", "gene_expression.tsv", package="Site2Target")
grs <- Table2Granges(fileName=geneFile,
                      chrColName="chr",
                       startColName="start",
                       endColName="end")
grs

Package 'Site2Target'

Help Index

Add column to gene-wise association

Description

Usage

Arguments

Value

See Also

Examples

Add a relation column to gene-peak interaction table

Description

Usage

Arguments

Value

See Also

Examples

MEIS cardiomyocytes datasets used in the package

Description

Format

Value

Examples

Extend sites given regions boundaries

Description

Usage

Arguments

Value

Examples

Generate genewise association between genes and peaks

Description

Usage

Arguments

Value

Examples

Return center of the given granges files

Description

Usage

Arguments

Value

Examples

Get names of genes or peaks related to a query coordinates

Description

Usage

Arguments

Value

generate number of sites per gene given distances

Description

Usage

Arguments

Value

Examples

Fit Negative binomial distribution to target genes

Description

Usage

Arguments

Value

Examples

Fit Negative binomial distribution to target genes

Description

Usage

Arguments

Value

Examples

Fit log-normal distribution to target genes

Description

Usage

Arguments

Value

Examples

Fit log-normal distribution to target genes

Description

Usage

Arguments

Value

Examples

Convert granges to strings of coordinates

Description

Usage

Arguments

Value

Examples