DE_Input
(Package: MEDIPSData) :
control data set from definitive endoderm
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"
DE_MeDIP
(Package: MEDIPSData) :
Concatenated set of three MeDIP-seq data sets (replicates) from definitive endoderm
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"
hESCs_Input
(Package: MEDIPSData) :
control data set from human embryonic stem cells
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"
hESCs_MeDIP
(Package: MEDIPSData) :
Concatenated set of three MeDIP-seq data sets (replicates) from human embryonic stem cells
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"
mart_gene
(Package: MEDIPSData) :
An annotation object generated by accessing biomaRt using the MEDIPS.getAnnotation function of the MEDIPS package.
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.
resultTable
(Package: MEDIPSData) :
A result table as returnced by the MEDIPS.meth function of the MEDIPS package
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.
providing 
.