gcompute_strands_autocorr: Computes auto-correlation between the strands for a file of...

In misha: Toolkit for Analysis of Genomic Data

Computes auto-correlation between the strands for a file of mapped sequences

Description

Calculates auto-correlation between plus and minus strands for the given chromosome in a file of mapped sequences.

Usage

gcompute_strands_autocorr(
  file = NULL,
  chrom = NULL,
  binsize = NULL,
  maxread = 400,
  cols.order = c(9, 11, 13, 14),
  min.coord = 0,
  max.coord = 3e+08
)

Arguments

file	the name of the file containing mapped sequences
chrom	chromosome for which the auto-correlation is computed
binsize	calculate the auto-correlation for bins in the range of [-maxread, maxread]
maxread	maximal length of the sequence used for statistics
cols.order	order of sequence, chromosome, coordinate and strand columns in file
min.coord	minimal coordinate used for statistics
max.coord	maximal coordinate used for statistics

Details

This function calculates auto-correlation between plus and minus strands for the given chromosome in a file of mapped sequences. Each line in the file describes one read. Each column is separated by a TAB character.

The following columns must be presented in the file: sequence, chromosome, coordinate and strand. The position of these columns are controlled by 'cols.order' argument accordingly. The default value of 'cols.order' is a vector (9,11,13,14) meaning that sequence is expected to be found at column number 9, chromosome - at column 11, coordinate - at column 13 and strand - at column 14. The first column should be referenced by 1 and not by 0.

Coordinates that are not in [min.coord, max.coord] range are ignored.

gcompute_strands_autocorr outputs the total statistics and the auto-correlation given by bins. The size of the bin is indicated by 'binsize' parameter. Statistics is calculated for bins in the range of [-maxread, maxread].

Value

Statistics for each strand and auto-correlation by given bins.

Examples

gdb.init_examples()
gcompute_strands_autocorr(paste(.misha$GROOT, "reads", sep = "/"),
    "chr1", 50,
    maxread = 300
)

misha documentation built on Sept. 14, 2023, 5:08 p.m.