gsegment: Divides track expression into segments

In misha: Toolkit for Analysis of Genomic Data

Divides track expression into segments

Description

Divides the values of track expression into segments by using Wilcoxon test.

Usage

gsegment(
  expr = NULL,
  minsegment = NULL,
  maxpval = 0.05,
  onetailed = TRUE,
  intervals = NULL,
  iterator = NULL,
  intervals.set.out = NULL
)

Arguments

expr	track expression
minsegment	minimal segment size
maxpval	maximal P-value that separates two adjacent segments
onetailed	if 'TRUE', Wilcoxon test is performed one tailed, otherwise two tailed
intervals	genomic scope for which the function is applied
iterator	track expression iterator of "fixed bin" type. If 'NULL' iterator is determined implicitly based on track expression.
intervals.set.out	intervals set name where the function result is optionally outputted

Details

This function divides the values of track expression into segments, where each segment size is at least of 'minsegment' size and the P-value of comparing the segment with the first 'minsegment' values from the next segment is at most 'maxpval'. Comparison is done using Wilcoxon (also known as Mann-Whitney) test.

If 'intervals.set.out' is not 'NULL' the result is saved as an intervals set. Use this parameter if the result size exceeds the limits of the physical memory.

Value

If 'intervals.set.out' is 'NULL' a set of intervals where each interval represents a segment.

See Also

gscreen, gwilcox

Examples

gdb.init_examples()
gsegment("dense_track", 5000, 0.0001)

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