GenCAT_manhattan: Create Manhattan Plot of GenCAT Results
In GenCAT: Genetic Class Association Testing

Description Usage Arguments Details Author(s) Examples

View source: R/GenCAT_functions.R

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

1
2
3

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

`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.

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

Eric Reed, Sara Nunez, Jing Qian, Andrea Foulkes

###############
#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)