[R] replacement has 0 rows, data has 2809

[Humberto Munoz Barona]

I am running the following R-code 

countToTpm <- function(counts, effLen)
{
  rate <- log(counts) - log(effLen)
  denom <- log(sum(exp(rate)))
  exp(rate - denom + log(1e6))
}

countToFpkm <- function(counts, effLen)
{
  N <- sum(counts)
  exp( log(counts) + log(1e9) - log(effLen) - log(N) )
}

fpkmToTpm <- function(fpkm)
{
  exp(log(fpkm) - log(sum(fpkm)) + log(1e6))
}

countToEffCounts <- function(counts, len, effLen)
{
  counts * (len / effLen)
}
################################################################################
# An example
################################################################################
data1 <- read.delim("Dark Aerobic1.csv", check.names=FALSE, stringsAsFactors=FALSE)
cnts <- data1['ReadCount']
lens <- data1['Length']
countDf <- data.frame(count = cnts, length = lens)

 # assume a mean(FLD) = 170.71

countDf$effLength <- countDf$length - 170.71 + 1
countDf$tpm <- with(countDf, countToTpm(count, effLength))
countDf$fpkm <- with(countDf, countToFpkm(count, effLength))
with(countDf, all.equal(tpm, fpkmToTpm(fpkm)))
countDf$effCounts <- with(countDf, countToEffCounts(count, length, effLength))

 I am receiving the errors

> countDf$effLength <- countDf$length - 170.71 + 1
Error in `$<-.data.frame`(`*tmp*`, "effLength", value = numeric(0)) : 
  replacement has 0 rows, data has 2809
> countDf$tpm <- with(countDf, countToTpm(count, effLength))
Error in countToTpm(count, effLength) : object 'count' not found
> countDf$fpkm <- with(countDf, countToFpkm(count, effLength))
Error in countToFpkm(count, effLength) : object 'count' not found
> with(countDf, all.equal(tpm, fpkmToTpm(fpkm)))
Error in all.equal(tpm, fpkmToTpm(fpkm)) : object 'tpm' not found
> countDf$effCounts <- with(countDf, countToEffCounts(count, length, effLength))
Error in countToEffCounts(count, length, effLength) : 
  object 'count' not found
> 

Thanks for any help to fix this error

Humberto Munoz