gsegment: 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
)

Value

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

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.

Examples

Run this code

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

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

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