As agstudy implied blat$LRwAvg <- as.character(blat$LRwAvg)
before loop fixed it
blat$meanLRwAvg <- blat$gtFrqAvg #or some other variable in data frame with equal length
blat$LRwAvg <- as.character(blat$LRwAvg)
for (i in 1:50){
y <- as.numeric(unlist(strsplit(blat$LRwAvg[i], "\\:")))
blat$meanLRwAvg[i]=mean(y)
}