Package 'MEDIPSData'

QSEA example annotation

Description

This is a list of GRange objects, which contain genomic annotations for hg19 reference, obtained from UCSC table browser.

Usage

data(annotation)

Examples

## Not run: 
data(annotation)
library(GenomicRanges)
names(ROIs)
ROIs$'gene body'
names(tfbs)

## End(Not run)

---

COUPLING SET

Description

This is a CpG coupling set generated by the MEDIPS package based on the human chromosome 22 (hg19) and with a window size of 100bp.

Usage

data(CS)

Examples

## Not run: 
data(CS)
library(MEDIPS)
CS

## End(Not run)

---

control data set from definitive endoderm

Description

This is a MEDIPS SET object created from Input-seq control data derived from definitive endoderm as presented by Chavez et al. 2010. The parameter settings are: BSgenome= "BSgenome.Hsapiens.UCSC.hg19" extend= 300 shift= 0 uniq= T ws= 100 chr.select= "chr22"

Usage

data(DE_Input)

References

Chavez, L., Jozefczuk, J., Grimm, C., Dietrich, J., Timmermann, B., Herwig, R., Adjaye, J. (2010): Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage, Genome Research. 20(10):1441-50

Examples

## Not run: 
data(DE_Input)
library(MEDIPS)
DE_Input

## End(Not run)

---

Concatenated set of three MeDIP-seq data sets (replicates) from definitive endoderm

Description

This is a concatenated set of three MEDIPS SET objects created from MeDIP-seq data derived from definitive endoderm as presented by Chavez et al. 2010. The parameter settings are: BSgenome= "BSgenome.Hsapiens.UCSC.hg19" extend= 300 shift= 0 uniq= T ws= 100 chr.select= "chr22"

Usage

data(DE_MeDIP)

References

Chavez, L., Jozefczuk, J., Grimm, C., Dietrich, J., Timmermann, B., Herwig, R., Adjaye, J. (2010): Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage, Genome Research. 20(10):1441-50

Examples

## Not run: 
data(DE_MeDIP)
library(MEDIPS)
DE_MeDIP

## End(Not run)

---

control data set from human embryonic stem cells

Description

This is a MEDIPS SET object created from Input-seq control data derived from human embryonic stem cells as presented by Chavez et al. 2010. The parameter settings are: BSgenome= "BSgenome.Hsapiens.UCSC.hg19" extend= 300 shift= 0 uniq= T ws= 100 chr.select= "chr22"

Usage

data(hESCs_Input)

References

Chavez, L., Jozefczuk, J., Grimm, C., Dietrich, J., Timmermann, B., Herwig, R., Adjaye, J. (2010): Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage, Genome Research. 20(10):1441-50

Examples

## Not run: 
data(hESCs_Input)
library(MEDIPS)
hESCs_Input

## End(Not run)

---

Concatenated set of three MeDIP-seq data sets (replicates) from human embryonic stem cells

Description

This is a concatenated set of three MEDIPS SET objects created from MeDIP-seq data derived from human embryonic stem cells as presented by Chavez et al. 2010. The parameter settings are: BSgenome= "BSgenome.Hsapiens.UCSC.hg19" extend= 300 shift= 0 uniq= T ws= 100 chr.select= "chr22"

Usage

data(hESCs_MeDIP)

References

Chavez, L., Jozefczuk, J., Grimm, C., Dietrich, J., Timmermann, B., Herwig, R., Adjaye, J. (2010): Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage, Genome Research. 20(10):1441-50

Examples

## Not run: 
data(hESCs_MeDIP)
library(MEDIPS)
hESCs_MeDIP

## End(Not run)

---

An annotation object generated by accessing biomaRt using the MEDIPS.getAnnotation function of the MEDIPS package.

Description

This is an annotation object generated by accessing biomaRt using the MEDIPS.getAnnotation function of the MEDIPS package: mart_gene = MEDIPS.getAnnotation(mart="ensembl", dataset=c("hsapiens_gene_ensembl"), annotation=c("GENE"), chr=22) The annotation object contains genomic coordinates of human genes on chromosome 22.

Usage

data(mart_gene)

Examples

## Not run: 
data(mart_gene)
data(resultTable)
library(MEDIPS)
resultTable = MEDIPS.setAnnotation(regions=resultTable, annotation=mart_gene)

## End(Not run)

---

QSEA MeDIP-seq lung cancer example dataset

Description

This is a qsea set object 'qseaSet' and a qsa glm object 'qseaGLM' qseaSet contains MeDIP seq data from NSCLC samples and adjacent normal. qseaGLM contains test statistics for the comparison of tumor and normal samples.

Usage

data(annotation)

Examples

## Not run: 
data(NSCLC_dataset)
library(qsea)
qseaSet
qseaGLM

## End(Not run)

---

A result table as returnced by the MEDIPS.meth function of the MEDIPS package

Description

This is a result table as returned by the MEDIPS.meth function using the following command: mr.edgeR = MEDIPS.meth(MSet1=hESCs, MSet2=DE, CSet=CS, ISet1=hESCs.Input, ISet2=DE.Input, p.adj="bonferroni", diff.method="edgeR", prob.method="poisson", CNV=F, MeDIP=T) where hESCs, DE, and CS are data objects included in this data package.

Usage

data(resultTable)

Examples

## Not run: 
data(resultTable)
library(MEDIPS)
mr.edgeR.s = MEDIPS.selectSig(results=mr.edgeR, p.value=0.05, adj=T, ratio=NULL, bg.counts=NULL, CNV=F)
mr.edgeR.s

## End(Not run)

---

QSEA lung cancer MeDIP seq sample table

Description

This data set contains a sample table describing the samples of the QSEA lung cancer MeDIP seq example data.

Usage

data(samplesNSCLC)

Examples

## Not run: 
data(samplesNSCLC)
samplesNSCLC

## End(Not run)

---

Lung cancer calibration data

Description

Calibration data for the lung cancer MeDIP seq example data, taken from TCGA LUAD and LUSC studies.

Usage

data(CS)

Examples

## Not run: 
data(tcga_luad_lusc_450kmeth)
tcga_luad_lusc_450kmeth

## End(Not run)

---