associateTFs2Exprs: Associate target genes to TFs and retrieve their expression

In GianlucaMattei/methyl.O: Annotate, Score and Visualize Differentially Methylated Regions

Associate target genes to TFs and retrieve their expression

Description

For each TF find and associate the target genes, within the annotation results, and retrieve expression

Usage

associateTFs2Exprs(
  annotatedDMRs,
  expressionProfile,
  active.features = c("promoters", "heads"),
  col.genes = 0,
  col.stat = 6,
  stat.thr = 0.05,
  col.logFC = 2,
  logfc.thr = 0,
  convert.genes = FALSE,
  convert.from,
  beta.thr = 0.3,
  overlap.param.thr = 30,
  param.type = "overlap.percentage"
)

Arguments

annotatedDMRs	anotated DMRs list resultingfrom annotateDMRs() or scoreAnnotatedDMRs()
expressionProfile	expression data.frame
active.features	character vectors containing features to correlate. Must be from names of resulting list from annotateDMRs. Additional feature names can be first exons (exons1) or first intron (intron1). To use more than one feature use c(). Default = c("promoters", "heads")
col.genes	numeric, the column of expressionProfile data.frame with gene Ids. If NULL geneIDs will be taken from rownames() of expressionProfile. Default = 0.
col.stat	numeric, the column of expressionProfile data.frame with the statistics to use. Default = 6.
stat.thr	numeric, threshold for statistical significance. Default = 0.05
col.logFC	numeric, the column of expressionProfile data.frame with log. fold change. Default = 2
logfc.thr	numeric, threshold value for log. fold change. Default = 0.
convert.genes	logical, used to indicate if gene ids have to be translated in official gene symbols. Default = FALSE
convert.from	character, used annotation for gene in expressionProfile to be converted to symbols gene IDs. Accepted: c("ENTREZID" ,"EXONID" ,"GENEBIOTYPE" ,"GENEID" ,"GENENAME" ,"PROTDOMID" ,"PROTEINDOMAINID" ,"PROTEINDOMAINSOURCE" ,"PROTEINID" ,""SEQSTRAND" ,"SYMBOL" ,"TXBIOTYPE" ,"TXID" ,"TXNAME" ,"UNIPROTID")
beta.thr	numeric, beta difference threshold value. Default = 0.3.
overlap.param.thr	numeric, threshold value for selected parameter to filter methylations overlapping the selected features. Default = 100
param.type	character, threshold parameter to filter methylations overlapping the selected features. Accetped c("dmr.length", "overlap.length", "overlap.percentage"). Default = "overlap.length".

Value

data.frame with TF methylation levels, target.genes expression

GianlucaMattei/methyl.O documentation built on Sept. 12, 2023, 11:53 p.m.