newSigInTAD: Create InTADSig object

Description Usage Arguments Details Value Examples

View source: R/InTADSig-methods.R

Description

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

Usage

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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 samples order 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

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

InTAD documentation built on Feb. 19, 2019, 2 a.m.