newSigInTAD {InTAD} | R Documentation

## Create InTADSig object

### 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)

[Package InTAD version 1.10.0 Index]