loadSigInTAD {InTAD} | R Documentation

## Load InTADSig object from text files

### 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)

[Package InTAD version 1.12.0 Index]