plot.GWAS: Significance plots and pvalues from 'gwas' output

In steibelj/gwaR: Functions for performing GWA from GBLUP

Description

Computes pvalues from a GWA class object represents them graphically. using manhattan_plot and qqgplot

Usage

## S3 method for class 'gwas'
plot(gwas, correction = "bonf", gpdata = NULL,
  plotlog10 = FALSE, pvalue = 0.05, q.qplot = FALSE, chrom = NULL, ...)

Arguments

gwas	an object of the class gwas generated by gwas
correction	a string with value 'bonf' if compute bonferroni correction is needed
gpdata	an object of class gpdata used to obtain a SNP map
plotlog10	a logical value indicating if a manhattan plot is requested
pvalue	significance threshold
q.qplot	a logical value indicating if a q-qplot is requested
...

Value

a vector of pvalues with names equal to marker names. Optional output: Manhattan plot and q-qplot of pvalues

steibelj/gwaR documentation built on May 30, 2019, 10:45 a.m.