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Get metagene at CDS

tx_get_metageneAtCDS.Rd

Get metagene at CDS

Usage

tx_get_metageneAtCDS(txDT, geneAnnot, colVars, CDS_align, upFlank, doFlank)

Arguments

txDT

data.table. A table as output by the tx_makeDT_coverage(), tx_makeDT_nucFreq() or tx_makeDT_covNucFreq() functions.

geneAnnot

GRanges. Gene annotation as loaded by tx_load_bed().

colVars

character. Names of columns for which values will be extracted

CDS_align

character. Either "start", "end", or "spliceSite" depending on the desired alignment, either to CDS start, CDS end, or splicing sites, respectively.

upFlank

numeric. Up-stream flank length

doFlank

numeric. Down-stream flank length

Value

list of matrices for each colVar