On 02/04/2014, 3:15 PM, Abugri James wrote:
I ran the following loop on my SNP data and got an error message as
indicated
I would assume that the error message is accurate:
as.character(current[1, "gene_old"]) has length zero. You'll need to
debug why that happened.
Duncan Murdoch
for (i in genenames){
+ current <- fst1[which(fst1$Gene == i),]
+ num <- nrow(current)
+ fst <- max(current$fst)
+ position <- mean(current$pos)
+ nposition <- mean(current$newpos)
+ numhigh <- nrow(current[which(current$fst > threshold),])
+ colors <- mean(current$colors)
+ output <- matrix(NA,nrow=1,ncol=8)
+ numthresh <- paste("# SNPs > Fst = ", threshold, sep="")
+ colnames(output) <- c("gene", "gene_old", "pos", "newpos", "# Snps",
numthresh, "Max.Fst", "colors")
+ output[1,1] <- i
+ output[1,2] <- as.character(current[1, "gene_old"])
+ output[1,3] <- position
+ output[1,4] <- nposition
+ output[1,5] <- num
+ output[1,6] <- numhigh
+ output[1,7] <- fst
+ output[1,8] <- colors
+ maxfstgene <- rbind(maxfstgene, output)
+ }
Error in output[1, 2] <- as.character(current[1, "gene_old"]) :
replacement has length zero
In addition: Warning message:
In mean.default(current$pos) :
argument is not numeric or logical: returning NA
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