newSigInTAD {InTAD} | R Documentation |
The fuction generates an object that contains the signals and gene expression data.frames along with their genomic coordinates for further processing.
newSigInTAD(signalData = NULL, signalRegions = NULL, countsData = NULL, geneRegions = NULL, sampleInfo = NULL, performLog = TRUE, logExprsOffset = 1, ncores = 1)
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 |
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.
Novel InTADSig object
## create sigInTAD object inTadSig <- newSigInTAD(enhSel, enhSelGR, rpkmCountsSel, txsSel)