[R] replacement has 0 rows, data has 2809

[Jim Lemon]

Hi Humberto,
It may simply be that the file is C(omma)SV format and the default
separator for read.delim is a TAB character. Try read.csv.

Jim


On Tue, Jun 21, 2016 at 2:14 AM, Humberto Munoz Barona
<hmunoz40 at hotmail.com> wrote:
> Hi Jim,
> Thanks for your reply. length(lens) gives me 6, which is the size of lens in the previous run with a shorter file. length(data1)=1, that means data1 is not reading the data from the file DarkAerobic1.CSV, which contains the four columns in this order Gene ID, Length, ReadCount, and Normalized Coverage. I want the vector lens = Length and cnts = ReadCounts. How I can make this import of data correctly?
>
>  > data1 <- read.delim("DarkAerobic1.CSV", check.names=FALSE, stringsAsFactors=FALSE)
>> lenght(data1)
> Error: could not find function "lenght"
>> length(data1)
> [1] 1
>
> I need to calculate two normalizations with the vectors lens and cnts, and have the two options for sorting the normalizations up or down.
>
> Thanks for any help you can give me to fix this issue.
>
> Humberto
>
>> On Jun 18, 2016, at 12:19 AM, Jim Lemon <drjimlemon at gmail.com> wrote:
>>
>> Hi Humberto,
>> The "0 row" error usually arises from a calculation in which a
>> non-existent object is used. I see that you have created a vector with
>> the name "lens" and that may be where this is happening. Have a look
>> at:
>>
>> length(lens)
>>
>> or if it is not too long, just:
>>
>> lens
>>
>> If it is zero length, that is your problem. This might be due to
>> "data1" not having a column named "Length" or it may not contain
>> numeric values (i.e. a factor)..
>>
>> Jim
>>
>>
>> On Sat, Jun 18, 2016 at 9:53 AM, Humberto Munoz Barona
>> <hmunoz40 at hotmail.com> wrote:
>>> 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
>>> ______________________________________________
>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>