contrastPlot: Contrast QCDH p values with single-SNP p values

In kindlychung/CollapsABEL: An R package for quantitative CDH analysis

Description

Contrast QCDH p values with single-SNP p values

Usage

contrastPlot(hub, chrfilter = NULL, bplower = NULL, bpupper = NULL,
  pvallower = NULL, pvalupper = NULL, bonferroni = FALSE)

Arguments

hub	QCDH data hub
chrfilter	Numeric. A vector of chromosome numbers. If present, then only SNPs in these chromosomes are selected. Default to NULL.
bplower	Numeric. If present, then only SNPs with base position greater than it will selected. Default to NULL.
bpupper	Numeric. If present, then only SNPs with base position less than it will selected. Default to NULL.
pvallower	Numeric. If present, then only SNPs with p values higher than it will be plotted in the single-SNP part. Default to NULL.
pvalupper	Numeric. If present, then only SNPs with p values lower than it will be plotted in the single-SNP part. Default to NULL.
bonferroni	Logical. If present, then the QCDH p values will be adjusted by Bonferroni correction. Default to NULL.

Value

A ggplot object of contrast Manhattan plot. (This plot is also stored in the QCDH data hub.)

kindlychung/CollapsABEL documentation built on May 20, 2019, 9:57 a.m.