loadSigInTAD: Load InTADSig object from text files

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

Description

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

Usage

loadSigInTAD(signalsFile, countsFile, gtfFile, annFile = "",
  performLog = TRUE, logExprsOffset = 1, ncores = 1)

Arguments

signalsFile	Tab-seprated data table containg signals and their coordinates as row.names
countsFile	Tab-seprated counts table
gtfFile	GTF file containing all gene coordinates
annFile	Tab-delimited phenotype annotation of samples
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

The function loads data from input files and creates object that stores matrices of signals and gene expression values along with coordiantes. The samples order and names of columns should match in both tables. It is expected that gene ids are applied in the validation of counts table.

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.