# #——回声= FALSE,结果=“隐藏”,警告= FALSE ------------------------------- suppressPackageStartupMessages({库(注释 ') }) ## ---- 回声= FALSE -------------------------------------------------------------- suppressPackageStartupMessages(图书馆(注释 )) ## ----------------------------------------------------------------------------- < - AnnotationHub中心 () ## ----------------------------------------------------------------------------- clinvar mcols(查询(中心。”vcf”、“GRCh37”)(“sourceurl”,放弃= FALSE ] ## ----------------------------------------------------------------------------- fl < -查询(clinvar中心。”vcf”、“GRCh37”)[[1 ]] ## ----------------------------------------------------------------------------- hg19“vcf < - readVcf (fl)暗(vcf ) ## ----------------------------------------------------------------------------- txdb_hg19 < - TxDb.Hsapiens.UCSC.hg19。knownGene头(seqlevels (txdb_hg19) seqlevels (vcf) seqlevels (vcf) < - paste0(“空空”,seqlevels (vcf )) ## ----------------------------------------------------------------------------- seqlevels (vcf pruning.mode =“粗”)< - c(“chr3”、“chr18”)seqlevels (txdb_hg19) < - c(“chr3”、“chr18 ") ## ----------------------------------------------------------------------------- 相交(seqlevels (txdb_hg19),seqlevels (vcf )) ## ----------------------------------------------------------------------------- 独特的基因组(txdb_hg19)独特(基因组(vcf )) ## ----------------------------------------------------------------------------- gr_hg19 < - rowRanges (vcf) ) ## ----------------------------------------------------------------------------- txdb_mm10 < - keepStandardChromosomes (TxDb.Mmusculus.UCSC.mm10.ensGene ) ## -----------------------------------------------------------------------------头(seqlevels (txdb_mm10)) gr_mm10 < -农庄(“chr4”,IRanges (c(4000000, 107889000),宽度= 1000 )) ## ----------------------------------------------------------------------------- 独特的(基因组(txdb_mm10))基因组(gr_mm10) <——“mm10 " ## ----------------------------------------------------------------------------- loc_hg19 < - locateVariants (gr_hg19、txdb_hg19 AllVariants())表(loc_hg19位置)美元loc_mm10 < locateVariants (gr_mm10 txdb_mm10,AllVariants表(loc_mm10 $())的位置 ) ## ----------------------------------------------------------------------------- 关口< - c(“UNIPROT”、“包含”)键< - na.omit(独特(loc_hg19 GENEID美元))头(select (org.Hs.eg.db、钥匙、关口,keytype = " ENTREZID ")) ## ----------------------------------------------------------------------------- 键< -独特(loc_mm10 GENEID美元)头(选择(org.Mm.eg.db、钥匙、关口,keytype = "运用 ")) ## ----------------------------------------------------------------------------- 中心< - AnnotationHub () hub_hg19 < -子集(中心(中心物种美元= =“智人”)&(中心基因组美元= =“hg19”))(hub_hg19长度 ) ## ---- 回声= FALSE -------------------------------------------------------------- ov_hg19 < -拉普(1:3,函数(我)subsetByOverlaps (hub_hg19[[我]],gr_hg19 )) ## ----------------------------------------------------------------------------- ov_hg19 < -拉普(1:3,函数(我)subsetByOverlaps (hub_hg19[[我]],gr_hg19 )) ## ----------------------------------------------------------------------------- 名称(ov_hg19) < -名称(hub_hg19)[1:3]拉普兰人(负责人ov_hg19, n = 3 ) ## ----------------------------------------------------------------------------- 头(predictCoding (vcf txdb_hg19 Hsapiens), 3) # #——税 --------------------------------------------------------------------- sessionInfo ()