pseudo_manhattan: Function to plot summary pseudo-manhattan plots of variants.

In AQS-Group/WISH: WISH

Description

Visualize summary statistics for interactions based on total sum of -loglikelihoods for each variant across all interactions og the sum of effect sizes.

Usage

pseudo_manhattan(tped,correlations,values="p")

Arguments

tped	Input tped file as .tped file or data frame. The tped file (.tped) is a transposed ped file, from Plink. This file contains the SNP and genotype information where one row is a SNP. The first 4 columns of a TPED file are the same as a 4-column MAP file. Then all genotypes are listed for all individuals for each particular SNP on each line. Again, SNPs are 1,2-coded.#'
correlations	List of epistatic correlations and p-values generated by epistatic.correlation()
values	Values can either be p or for p-values or c for coefficients depending on if you wan't to use the effects sizes for p-values for plotting

Value

Plots a pseudo manhattan plot

Examples

pseudo_manhattan(tped,correlations)

AQS-Group/WISH documentation built on July 17, 2020, 12:12 a.m.