wiggle_correlation: Correlation between two ChIP-seq experiments

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

Correlation between two ChIP-seq experiments

Description

This function allows you to calculate correlations between wiggle files for ChIP-seq, both on an individual chromosome basis and genome-wide. It takes as an input two lists of 16 chromosomes (output of readall_tab).

Usage

wiggle_correlation(Set1, Set2, method = "spearman")

Arguments

Set1	A list of 16 chr wiggle data (output of readall_tab)
Set2	A list of 16 chr wiggle data (output of readall_tab)
method	A character string indicating which correlation coefficient is to be computed (method argument to R function cor()). Accepts one of pearson (default), kendall, or spearman.

Value

A vector with 17 values with names indicating the chromosome associated with each individual correlation value.

Examples

## Not run: 
wiggle_correlation(Red1WT_rep1, Red1WT_rep2)

wiggle_correlation(Red1WT_rep1, Red1WT_rep2, method = "spearman")

## End(Not run)

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