loadSigInTAD: Load InTADSig object from text files

Description Usage Arguments Details Value Examples

View source: R/InTADSig-methods.R

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

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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

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

InTAD documentation built on Dec. 7, 2018, 6 p.m.