Hello,

Currently I am trying to load chr1 into a snp.matrix and from this matrix, I
am tring to calculate the "ld" between two snps, when I enter

>pair.result.ld.snp(chr1[[1]], 748682, 748704)

I get the following errors. Any clues here would help. SESSION_

Information: samples = 174, snps = 314024
 ii = 748682, jj = 748704

 *** caught segfault ***
address 0xb7f9153e, cause 'memory not mapped'

Traceback:
 1: .Call("snp_pairwise", snpdata, loc.snpA, loc.snpB, PACKAGE =
"snpMatrix")
 2: pair.result.ld.snp(chr1[[1]], 748682, 748704)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 1
aborting ...
Segmentation fault

> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: i686-pc-linux-gnu (32-bit)
locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] splines   stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] snpMatrix_1.14.6 survival_2.36-5


s

On Wed, Jun 29, 2011 at 10:31 PM, Vincent Carey
<stvjc@channing.harvard.edu>wrote:

>
>
> On Thu, Jun 30, 2011 at 2:04 AM, rna seq <rna.seeker@gmail.com> wrote:
>
>> Hello Bioconductor,
>>
>> I am having some difficulties using the "snpMatrix" package. I download
>> the
>> following file using:
>>
>> >chr1<-read.HapMap.data("
>>
>> http://hapmap.ncbi.nlm.nih.gov/downloads/genotypes/latest_phaseII+III_ncbi_b36/forward/non-redundant/genotypes_chr1_CEU_r27_nr.b36_fwd.txt.gz
>> "
>>
>> Next, I would like to calculate the linkage disequilibrium between these
>> snps. I then try to get the ld between these sample by typing
>>
>> >> ld.snp(chr1)
>>
>> and get the following error
>> Error in ld.snp(chr1) :
>>  snps argument must be of class snp.matrix/X.snp.matrix
>>
>>
> read.HapMap.data returns a list that includes a snp.matrix and some
> metadata support.  i believe
> that ld.snp(chr1[[1]]) would work
>
> use class(chr1), str(chr1) and str(chr1[[1]]) and so forth to diagnose such
> situations, and read the
> man page for read.* to understand fully the returned object
>
> also please supply sessionInfo() result for all queries.
>
>
>> This is confusing to me because the vignette tells me that
>> read.HapMap.data
>> will download and convert the genotype data into a snp.matrix class object
>>
>> Any help is greatly appreciated.
>>
>> Thanks,
>>
>> Pete
>>
>>        [[alternative HTML version deleted]]
>>
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>>
>
>

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