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_an alysis/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/ta bix") > 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, [[alternative HTML version deleted]]

you didn't give sessionInfo() result. but see below On Sun, Jun 12, 2011 at 6:33 AM, Mao Jianfeng <jianfeng.mao at="" gmail.com=""> wrote: > 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 that's because this is not a valid call to single.snp.tests -- read the doc on that function > >> snpsum<-col.summary(vcf2sm.test) > Error in col.summary(vcf2sm.test) : not a snp.matrix object this one is more difficult. we need to see your sessionInfo() result -- col.summary should not be asking for snp.matrix instance, but if you have chopsticks or an old snpMatrix package attached you could have such issues > > > Thanks in advance. > > Best > Jian-Feng, > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >