genome.interaction: Visualization of pairwise chromosome epistatic interactions...

Description Usage Arguments Value Examples

View source: R/all_functions.R

Description

Visualization of the genome wide chromosome pairwise relative strength of epistatic interaction, ranging from 1 (strongest) to 0 (weakest). The strength is based on the 90th percentile quantile (default) of stastistical significance of epistatic interaction between all interactions in each chromosome pair, scaled to 1 to 0.

Usage

1
genome.interaction(tped,correlations,quantile=0.9)

Arguments

tped

The tped file used in generate.genotype(). The SNPs must be sorted by chromosome, matching the order of the SNPs in the correlation matrices.

correlations

List of epistatic correlations and p-values genrated by epistatic.correlation()

quantile

Number from 0 to 1 indicating which quantile to base the visualization on.

Value

Outputs a plot visualizing the chromosome interaction map

Examples

1
 genome.interaction(tped,correlations)

QSG-Group/WISH documentation built on July 20, 2020, 2:11 p.m.