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library(ctl)
# The genotypes.csv file containing the genotype matrix is stored individuals (rows) x genetic marker (columns):
genotypes <- read.csv("genotypes.csv",row.names=1, header=FALSE, sep="\t")
# The phenotypes.csv file containing individuals (rows) x traits (columns) measurements:
traits <- read.csv("phenotypes.csv",row.names=1, header=FALSE, sep="\t")
ctls <- CTLscan(geno,traits,strategy=input$strategy,
nperm=input$nperms,parametric =input$parametric,
nthreads=6,verbose=TRUE)
#output matrix significant CTL interactions with 4 columns: trait, marker, trait, lod
sign <- CTLsignificant(ctls,significance = input$significance)
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