plotPmat {aSPU} | R Documentation |
It gives a P-value image for a given P-value matrix.
plotPmat(
Ps,
zlim = NULL,
main = NULL,
yt = NULL,
xlab = "SNPs",
thresh = -log(5e-08, 10),
trait.names = NULL
)
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. |
Image of P-values matrix.
Il-Youp Kwak and Wei Pan
Il-Youp Kwak, Wei Pan (2017) Gene- and pathway-based association tests for multiple traits with GWAS summary statistics, Bioinformatics. 33(1), 64-71
## 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)