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Calculate nucleotide frequency pileup for all gene models

hlp_nucFreqTab_mc.Rd

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:

  1. '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.

  2. "splitHalf': Ambiguous reads will be divided in half, in odd cases having fractions of reads assigned.

  3. "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