aSPU (version 1.50)

plotPmat: Image plot of P-value matrix.

Description

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

Usage

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.

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

# NOT RUN {
## 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)


# }