Dear all,
I have a .csv file called df4. (15752 obs. of 264 variables).
I apply this code but couldn't continue further other analyses, a warning
message keeps coming up. Then, I want to determine max and min
similarity values,
heat map plot, cluster...etc
> require(SNPRelate)
> library(gdsfmt)
> myd <- read.csv(file = "df4.csv", header = TRUE)
> names(myd)[-1]
myd[,1]
> myd[1:10, 1:10]
# the data must be 0,1,2 with 3 as missing so you have r
> sample.id <- names(myd)[-1]
> snp.id <- myd[,1]
> snp.position <- 1:length(snp.id) # not needed for ibs
> snp.chromosome <- rep(1, each=length(snp.id)) # not needed for ibs
> snp.allele <- rep("A/G", length(snp.id)) # not needed for ibs
# genotype data must have - in 3
> genod <- myd[,-1]
> genod[is.na(genod)] <- 3
> genod[genod=="0"] <- 0
> genod[genod=="1"] <- 2
> genod[1:10,1:10]
> genod <- as.matrix(genod)
> class(genod) <- "numeric"
*Warning message:In class(genod) <- "numeric" : NAs introduced by coercion*
Maybe I could illustrate more with details so I can be more specific?
Please, let me know.
I would appreciate your help.
Thanks,
Meriam
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