GenCAT (version 1.0.2)

GenCAT_manhattan: Create Manhattan Plot of GenCAT Results

Description

This function will create a Manhattan Plot from output of GenCAT function

Usage

GenCAT_manhattan(GenCATout, sigThresh = NULL, highlightPosi = FALSE,
labelPosi = FALSE, sepChr = 8e+05,  
plotTitle = "Manhattan Plot of GenCAT Results")

Arguments

GenCATout

An object of class, GenCATtest.

sigThresh

P-value threshold to highlight classes with strong signal from GenCAT test

highlightPosi

logical. If TRUE, classes with GenCAT p-value less than sigThresh will be shown in blue

labelPosi

logical. If TRUE, classes with GenCAT p-value less than sigThresh will be labelled.

sepChr

Specifies the space to put between chromosomes on the plot.

plotTitle

Character expression for plot title.

Details

GenCATtest is the class of the output of the GenCAT function.

Examples

###############
#Running GenCAT
###############
data("CardioMapped")

#Subset CardioMapped to decrease CPU time
CardioMappedSub<-CardioMapped[CardioMapped$chr < 15,]
set.seed(1)
CardioMappedSub<-CardioMappedSub[sample(1:nrow(CardioMappedSub), 100),]

library(snpStats)
data('geno')

genoData<-geno$genotypes
snpInfo<-geno$map

colnames(snpInfo)<-c('chr', 'SNP', 'gen.dist', 'position', 'A1', 'A2')
print(head(snpInfo))

GenCATtest <- GenCAT(CardioMappedSub, genoData=genoData, snpInfo = snpInfo)

######################
#Create Manhattan Plot
######################

print(str(GenCATtest))
GenCAT_manhattan(GenCATtest, sigThresh = (0.05/nrow(GenCATtest$GenCAT)), 
highlightPosi = TRUE, labelPosi = TRUE)