[BioC] htSeqTools errors

[Valerie Obenchain]

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
>
>