[BioC] htSeqTools errors

[Juan L. Mateo]

Hi Valerie,

Thanks for you answer.
This object contains 16M reads and I am happy to provide any information 
that would be useful or even this object which is 206Mb big.

 > sapply(samples,nrow)
Con_input
  16513449

Best,
Juan

On 02/20/2012 08:08 PM, Valerie Obenchain wrote:
> Hi Juan,
>
> ccing the author in case he hasn't seen this.
>
> Can you provide more information on what 'samples' looks like or the
> object itself?
>
> Valerie
>
>
>
>
> On 02/16/12 04:51, Juan L. Mateo wrote:
>> Hi all,
>>
>> I am trying to use htSeqTools to analyse some ChIP-seq samples and I
>> am getting errors on the methods cmds and giniCoverage. Below I paste
>> the output of a session.
>>
>> Any help will be greatly appreciated.
>>
>>
>> > what=c("rname", "strand", "pos", "qwidth")
>> > param=ScanBamParam(what = what)
>> >
>> > Con_input<-scanBam('Con_input.fastq.bam', param=param)[[1]]
>> >
>> Con_input.reads<-GRanges(seqnames=Rle(Con_input$rname),ranges=IRanges(Con_input$pos,
>> width=Con_input$qwidth))
>> > samples<-RangedDataList(Con_input=as(Con_input.reads,"RangedData"))
>> > cmds1<-cmds(samples,k=2)
>> Computing coverage...
>> Computing correlations...
>> Error in d[[i]] : subscript out of bounds
>> > ssdCoverage(samples)
>> Con_input
>> 0.2551517
>> > giniCoverage(samples,mc.cores=1)
>> Simulating uniformily distributed data
>> Error in sample.int(chrLen[i], as.integer(chrReads[i]), replace = T) :
>> invalid 'size' argument
>> In addition: Warning messages:
>> 1: In FUN(X[[1L]], ...) : no non-missing arguments to max; returning -Inf
>> 2: In FUN(X[[1L]], ...) : no non-missing arguments to max; returning -Inf
>> 3: In FUN(X[[1L]], ...) : no non-missing arguments to max; returning -Inf
>> 4: In eval(expr, envir, enclos) : NAs introduced by coercion
>>
>>
>>
>>
>> > sessionInfo()
>> R Under development (unstable) (2012-02-13 r58337)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>> [1] LC_CTYPE=en_GB LC_NUMERIC=C LC_TIME=en_GB
>> [4] LC_COLLATE=en_GB LC_MONETARY=en_GB LC_MESSAGES=en_GB
>> [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
>> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] htSeqTools_1.1.2 BSgenome_1.23.2 MASS_7.3-17
>> [4] Biobase_2.15.3 Rsamtools_1.7.33 Biostrings_2.23.6
>> [7] GenomicRanges_1.7.24 IRanges_1.13.24 BiocGenerics_0.1.4
>>
>> loaded via a namespace (and not attached):
>> [1] bitops_1.0-4.1 zlibbioc_1.1.1
>>
>>
>