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

In victorcarmelo/WISH: Network construction of whole genome genotype data using the WISH network method

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). By defaulty chromosomes are separated into 1 Mb regions, but if SNPs are more spaced out that this it will adjust to the smallest region that fit the data.

Usage

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

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(). 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()
span	Region in bp. Default is 1 Mb (10^6)

Value

Outputs a plot visualizing the pairwise chromosome region interaction

Examples

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

victorcarmelo/WISH documentation built on May 3, 2019, 6:11 p.m.