hlp_nucFreqTab_mc: Calculate nucleotide frequency pileup for all gene models

In AngelCampos/txtools: An R package facilitating analysis of RNA modifications, structures, and interactions

Calculate nucleotide frequency pileup for all gene models

Description

Calculate nucleotide frequency pileup for all gene models

Usage

hlp_nucFreqTab_mc(x, simplify_IUPAC = "not", nCores)

Arguments

x	CompressedGRangesList. Genomic Ranges list containing genomic alignments data by gene. Constructed via tx_reads().
simplify_IUPAC	character. Method to simplify ambiguous reads: 'not': Ambiguous reads will be left as their IUPAC_ambiguous code, e.g. for positions in which a 'G' and and 'A' where read an 'R' will note this. "splitHalf': Ambiguous reads will be divided in half, in odd cases having fractions of reads assigned. "splitForceInt": Ambiguous reads will be divided in half, but forced to be integers, unassigned fraction of reads will be summed and assigned as 'N'.
nCores	integer. Number of cores to run the function with. Multicore capability not available in Windows OS.

Value

data.table

AngelCampos/txtools documentation built on April 8, 2024, 6:06 p.m.