代码如下：
> head(dat) Composite.Element.REF Call Confidence 1 SNP_A-2131660 2 0.0126 2 SNP_A-1967418 2 0.0029 3 SNP_A-1969580 2 0.0019 4 SNP_A-4263484 2 0.0043 5 SNP_A-1978185 0 0.0082 6 SNP_A-4264431 1 0.0088 > library(BiocInstaller) Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help > biocLite("pd.genomewidesnp.6") > library(pd.genomewidesnp.6) > con <- pd.genomewidesnp.6@getdb() > dbListTables(con) [1] "featureSet" "featureSetCNV" "fragmentLength" "fragmentLengthCNV" "pmfeature" "pmfeatureCNV" [7] "sequence" "sequenceCNV" "sqlite_stat1" "table_info" > dbGetQuery(con, "select * from featureSet limit 3")[,1:10] fsetid man_fsetid affy_snp_id dbsnp_rs_id chrom physical_pos strand cytoband allele_a allele_b 1 1 SNP_A-2131660 NA rs2887286 1 1156131 0 p36.33 C T 2 2 SNP_A-1967418 NA rs1496555 1 2234251 0 p36.33 A G 3 3 SNP_A-1969580 NA rs41477744 1 2329564 0 p36.32 A G > dim(dat) [1] 906600 3 > anno <- dbGetQuery(con, "select * from featureSet") > dim(anno) [1] 906600 13 > data <- cbind(dat, anno[match(dat[,1], anno[,2]),]) > dim(data) [1] 906600 16 > miR146a <- data[grepl("miR146a", data[,"gene_assoc"], ignore.case=T), ] > dim(miR146a) [1] 49 16 > head(data[,1:13]) Composite.Element.REF Call Confidence fsetid man_fsetid affy_snp_id dbsnp_rs_id chrom physical_pos strand cytoband allele_a allele_b 1 SNP_A-2131660 2 0.0126 1 SNP_A-2131660 NA rs2887286 1 1156131 0 p36.33 C T 2 SNP_A-1967418 2 0.0029 2 SNP_A-1967418 NA rs1496555 1 2234251 0 p36.33 A G 3 SNP_A-1969580 2 0.0019 3 SNP_A-1969580 NA rs41477744 1 2329564 0 p36.32 A G 4 SNP_A-4263484 2 0.0043 4 SNP_A-4263484 NA rs3890745 1 2553624 0 p36.32 C T 5 SNP_A-1978185 0 0.0082 5 SNP_A-1978185 NA rs10492936 1 2936870 1 p36.32 C T 6 SNP_A-4264431 1 0.0088 6 SNP_A-4264431 NA rs10489588 1 2951834 1 p36.32 C T > miR146a[miR146a$dbsnp_rs_id=="rs2910164",1:13] Composite.Element.REF Call Confidence fsetid man_fsetid affy_snp_id dbsnp_rs_id chrom physical_pos strand cytoband allele_a allele_b 283011 SNP_A-2264525 0 0.0012 283011 SNP_A-2264525 NA rs2910164 5 159912418 1 q34 C G |
