misha (version 4.2.9)

gcompute_strands_autocorr: 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
)

Value

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

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].

Examples

# \dontshow{
options(gmax.processes = 2)
# }

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