gwilcox: Calculates Wilcoxon test on sliding windows over track...

In misha: Toolkit for Analysis of Genomic Data

Calculates Wilcoxon test on sliding windows over track expression

Description

Calculates Wilcoxon test on sliding windows over the values of track expression.

Usage

gwilcox(
  expr = NULL,
  winsize1 = NULL,
  winsize2 = NULL,
  maxpval = 0.05,
  onetailed = TRUE,
  what2find = 1,
  intervals = NULL,
  iterator = NULL,
  intervals.set.out = NULL
)

Arguments

expr	track expression
winsize1	number of values in the first sliding window
winsize2	number of values in the second sliding window
maxpval	maximal P-value
onetailed	if 'TRUE', Wilcoxon test is performed one tailed, otherwise two tailed
what2find	if '-1', lows are searched. If '1', peaks are searched. If '0', both peaks and lows are searched
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 runs a Wilcoxon test (also known as a Mann-Whitney test) over the values of track expression in the two sliding windows having an identical center. The sizes of the windows are specified by 'winsize1' and 'winsize2'. 'gwilcox' returns intervals where the smaller window tested against a larger window gives a P-value below 'maxpval'. The test can be one or two tailed.

'what2find' argument controls what should be searched: peaks, lows or both.

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 data frame representing the intervals with an additional 'pval' column where P-value is below 'maxpval'.

See Also

gscreen, gsegment

Examples

gdb.init_examples()
gwilcox("dense_track", 100000, 1000,
    maxpval = 0.01,
    what2find = 1
)

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