Dear all,

# (1) my problem:
*I would like to get your helps on how to convert GGtools object (generated
by vcf2sm) to snpMatrix class or other class (like classes used in R
packages adegenet and genetics)*. Are there already anything functionalities
implemented in R or bioconductor.

# (2) background

I am working on VCF format for population genomic studies. I would like to
take advantage of R/bioconductor.

Under helps from bioconductor, I have now can covert my VCF files to a
SnpMatrix by using vcf2sm in GGtools package.

# (3) my VCF data

my VCF data are not normal genotypic data, they are haplotypic data (like
SNP data from X or Y chromosomes of human).

# (4) codes I have ever used

library(GGtools)
library(snpMatrix)

vcf2sm.test<-vcf2sm(gzpath="/ebio/abt6_projects5/backup/data/solexa_analysis/Lyrata/F1_seq_sam/non_heterozygous/merged_data/euro_head.vcf.gz",
chrom="1",
tabixcmd="/ebio/abt6_projects/backup/solexa_tools/tabix/tabix-0.2.3/tabix")

> vcf2sm.test
A SnpMatrix with  20 rows and  1985 columns
Row names:  AL23C2_3 ... AL34C1-2
Col names:  chr1:69 ... chr1:83679

> str(vcf2sm.test)
Formal class 'SnpMatrix' [package "snpStats"] with 1 slots
  ..@ .Data: raw [1:20, 1:1985] 02 02 02 02 ...
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:20] "AL23C2_3" "AL23C2_1" "AL14C5P2-2" "AL10C3-P1-1"
...
  .. .. ..$ : chr [1:1985] "chr1:69" "chr1:87" "chr1:88" "chr1:116" ...

> single.snp.tests(vcf2sm.test)
Error in class(object) : 'object' is missing

> snpsum<-col.summary(vcf2sm.test)
Error in col.summary(vcf2sm.test) : not a snp.matrix object


Thanks in advance.

Best
Jian-Feng,

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