misha (version 4.2.9)

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.

See Also

gscreen, gwilcox

Examples

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

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