convert_to_counted: convert to counted GRanges

In rmflight/fmcorrelationbreastcaparp1: Functions for calculating the correlations in PARP1 nucleosome data in breast cancer cell lines

Description

given a set of reads in a delimited file, find the unique locations, count the number of reads at each location, apply a hard threshold if required, and save the data to an RData file.

Usage

convert_to_counted(reads_file, delim = ",", read_start = "startx",
  width = 1, strand = "strand", scramble_strand = TRUE, max_count = 6,
  prepend = "")

Arguments

reads_file	the file with the reads
delim	the delimiter to use
read_start	the column containing the read starts
width	how wide are the reads
strand	which column name has the strand information
scramble_strand	should the strand be scrambled (default is TRUE)
max_count	what is the maximum value that the counts should be
prepend	text to prepend the out_file name with

Value

the RData filename

rmflight/fmcorrelationbreastcaparp1 documentation built on May 27, 2019, 9:31 a.m.