plotPmat: Image plot of P-value matrix.

Description Usage Arguments Value Author(s) References See Also Examples

Description

It gives a P-value image for a given P-value matrix.

Usage

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plotPmat(Ps, zlim = NULL, main = NULL, yt = NULL, xlab = "SNPs",
  thresh = -log(5e-08, 10), trait.names = NULL)

Arguments

Ps

P-value matrix. Row represent traits, column represent SNPs

zlim

-log 10 transformed p value range.

main

main title.

yt

it controls the location of trait names.

xlab

lable for x axis. Default is "SNPs".

thresh

Default is set to widely used genome wise threshold -log(5e-8,10).

trait.names

A vector of trait names.

Value

Image of P-values matrix.

Author(s)

Il-Youp Kwak and Wei Pan

References

Il-Youp Kwak, Wei Pan (2017) Gene- and pathway-based association tests for multiple traits with GWAS summary statistics, Bioinformatics. 33(1), 64-71

See Also

aSPUs

Examples

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## Say we have 3 traits and their p-values at 5 SNPs. 
Ps <- rbind( c(0.001, 0.4, 0.5, 0.00000001, .1),
           c(0.03, 0.3, 0.3, 0.00001, .2),
           c(0.01, 0.2, 0.4, 0.001, .0001) )

## We can visualize it using plotPmat function.
plotPmat(Ps)

aSPU documentation built on May 1, 2019, 7:04 p.m.