pairwise.chr.map: Visualization of chromosomal pairwise region epistatic...

Description Usage Arguments Value Examples

View source: R/all_functions.R

Description

Visualization of chromosome pairwise region epistatic interaction strength, based on statistical significance. The value is based of the most signficant epistatic interaction in each region pair, ranging from 1 ( strongest) to 0 (weakest). The original input data and tped file needs to be sorted by chromosome and coordinate.

Usage

1
pairwise.chr.map(chr1,chr2,tped,correlations,50)

Arguments

chr1

The name of the first chromosome in the comparison, matching the name from the tped file

chr2

The name of the second chromosome in the comparison, matching the name from the tped file

tped

The tped file used in generate.genotype(), either as a datafrae or filelink. The SNPs must be sorted by chromosome and position on the chromosome, matching the order of the SNPs in the correlation matrices.

correlations

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

grid_size

Number of regions to split each chromosome. This value is approximate as the number variants is not always easily divisible by the number of splits. The actual number of regions are displayed in the output plot

Value

Outputs a plot visualizing the pairwise chromosome region interaction

Examples

1
 pairwise.chr.map("1","2",tped,correlations)

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