Hi Juan,

we have been working on the giniCoverage function regarding several issues
that arised with version 1.0 of the package. They are already available in
the development version of the package available from the Bioconductor
development repository. Please let me know should you have doubts or
experience problems installing that version.

As for the cmds function, from your code I assume your data is basically a
single sequencing sample, whereas the idea behind the cmds function is to
produce a pca-like plot showing separation and relative positioning of
several samples to assess their similarities. Nonetheless I'm not sure if
the error you are getting is due to that, and would be grateful if you
could give me access to your .bam file is possible so I can try to
reproduce the error here.

Best regards,

Oscar

On Tue, Feb 21, 2012 at 10:12 AM, Juan L. Mateo <
juan.mateo@cos.uni-heidelberg.de> wrote:

> 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
>>>
>>>
>>>
>>


-- 
Oscar Reina
Research officer, Bioinformatics and Biostatistics unit
IRB Barcelona
Cluster building, PBC32
Tel (+34) 93 402 0553
Fax (+34) 93 402 0257

oscar.reina@irbbarcelona.org
http://www.irbbarcelona.org/bioinformatics

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