ntfreq: ntfreq

In ssviz: A small RNA-seq visualizer and analysis toolkit

Description

Calculates nucleotide frequency of reads in bam file

Usage

ntfreq(bam_file, ntlength, toRNA = TRUE, count_type = "total")

Arguments

bam_file	An object of class data.frame or DataFrame
ntlength	An integer specifying the length of the sequence to quantify
toRNA	A logical value on whether to translate the DNA sequence to RNA
count_type	A character string on how to count the nucleotides. Can be either "total" or "unique". If total is selected, the function will look for the countcolumn and multiply the reads by its number of occurence when calculating the frequency.

Value

Returns a data.frame of the frequency of nucleotides (either A/C/G/T or A/C/G/U) at each position up to the specified ntlength

Author(s)

Diana H.P. Low

Examples

data(ssviz)
freq<-ntfreq(pctrlbam,ntlength=10)

ssviz documentation built on Nov. 8, 2020, 5:53 p.m.