[BioC] snpMatrix trouble with read.HapMap.data() and ld.snp()

David Clayton dc208 at cam.ac.uk
Thu Jun 30 10:46:21 CEST 2011

read.HapMap.data() does not return an object of class "snp.matrix". It 
returns a list whose first element is the snp.matrix object. See the 
online help page

On 30/06/11 01:04, rna seq 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
> 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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Professor David Clayton
Wellcome Trust/Juvenile Diabetes Research Foundation Principal Research 

Diabetes and Inflammation Laboratory
Cambridge University, Department of Medical Genetics
Cambridge Institute for Medical Research
Wellcome Trust/MRC Building
Addenbrooke's Hospital
Hills Road

Tel: (44) 1223 762669
Email: david.clayton at cimr.cam.ac.uk

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