newSigInTAD: Create InTADSig object

In kokonech/InTAD: Search for correlation between epigenetic signals and gene expression in TADs

Description

The fuction generates an object that contains the signals and gene expression data.frames along with their genomic coordinates for further processing.

Usage

newSigInTAD(signalData = NULL, signalRegions = NULL, countsData = NULL,
  geneRegions = NULL, sampleInfo = NULL, performLog = TRUE,
  logExprsOffset = 1, ncores = 1)

Arguments

signalData	data frame containing signals
signalRegions	genomic regions of the signals
countsData	data matrix containing count expression values
geneRegions	gene coordiantes
sampleInfo	data frame containing additional sample info
performLog	Perform log2 convertion of expression values. Default: TRUE.
logExprsOffset	Offset x for log2 gene exrpression i.e. log2(value + x). Default: 1
ncores	Number of cores to use for parallel computing

Details

InTADSig object stores matrices of signals and gene expression values along with coordinates. The order of samples and names of columns should match in both datasets. For gene coordinates GRanges "gene_id" and "gene_name" are required in metadata. These are typical markers of genes in GTF anntotation format.

Value

Novel InTADSig object

Examples

## create sigInTAD object
inTadSig <- newSigInTAD(enhSel, enhSelGR, rpkmCountsSel, txsSel)

kokonech/InTAD documentation built on Jan. 1, 2021, 9:23 p.m.