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

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