wiggle_compress: Compress wiggle data

In hochwagenlab/hwglabr: Collection of R functions used in the Hochwagen Lab

Compress wiggle data

Description

This function will compress wiggle data by averaging values (including position) across non-overlapping windows. It will take any number of wiggle files, but can only handle one chromosome or chromosomal region per function call. This function assumes that all data is from the chromosome and ignores all chromosomal information. This function ignores all positions without reads mapping which may lead to slight variations in position depending on the wiggle data being used. Note: calls function compress.
Written by Tovah Markowitz.

Usage

wiggle_compress(inputWiggles, window)

Arguments

inputWiggles	Will accept two types of wiggle information: A single wiggle region/chromosome Multiple wiggle files to be directly compared/compressed. These must be listed as strings in the following format: c("wiggleData1[[chr]]", "wiggleData2[[chr]]", ...).
window	Size of window to be averaged across. Suggested size for chromosome-wide plots for presenting and publication: 200 bp. No default.

Value

A R (dplyr) data frame with averaged position and value for each wiggle. Column names are defined by input strings/variables.

Examples

## Not run: 
wiggle_compress( red1[[6]], 200 )

wiggle_compress( c( "red1[[6]]", "hop1[[6]]", "smc4[[6]]" ), 200 )

## End(Not run)

hochwagenlab/hwglabr documentation built on Feb. 25, 2025, 5:41 a.m.