Hello
I am recently using FarmCPU for my GWAS analysis. Whenever I quote command of covariate variable (PCA) that gives error message as below.
setwd("C:\\myFarmCPU")
myY <- read.table("mdp_traits_validation.txt", head = TRUE)
myGM <- read.table("mdp_SNP_information.txt", head = TRUE)
myGD <- read.big.matrix("mdp_numeric.txt", type="char", sep="\t", head = TRUE)
myCV <- read.table("Copy of Q_First_Three_Principal_Components.txt", head = TRUE)
myFarmCPU <- FarmCPU(
Y=myY[,c(1,8)],
GD=myGD,
GM=myGM,
CV=myCV
)
[1] "--------------------- Welcome to FarmCPU ----------------------------"
[1] "FarmCPU Started..."
[1] "Current loop: 1 out of maximum of 10"
[1] "seqQTN"
NULL
[1] "scanning..."
[1] "number of covariates in current loop is:"
[1] 4
[1] "Current loop: 2 out of maximum of 10"
[1] "optimizing possible QTNs..."
[1] "Top snps have little effect, set seqQTN to NULL!"
Error in seq.default(1, nchr, by = ncycle) : invalid '(to - from)/by'
Kindly suggest me solution for this