我有一个名为mydf的数据框。我想寻找中存在c.change
值Clinvar_Type
。如果存在,我想删除中的所有内容grepl("Clinvar, colnames(mydf))
。
这是我的数据:
mydf <- structure(c("chr1:8045045:A:G", "chr1:8045045:A:G", "chr1:8045045:A:G",
"chr1:17314702:C:T", "chr1:17314702:C:T", "chr1:17314702:C:T",
"c.501A>G", "c.441A>G", "c.414A>G", "c.2775G>A", "c.2658G>A",
"c.2790G>A", "NM_007262.5(PARK7):c.501A>G (p.Ala167=)", "NM_007262.5(PARK7):c.501A>G (p.Ala167=)",
"NM_007262.5(PARK7):c.501A>G (p.Ala167=)", "NM_022089.4(ATP13A2):c.2790G>A (p.Ser930=)",
"NM_022089.4(ATP13A2):c.2790G>A (p.Ser930=)", "NM_022089.4(ATP13A2):c.2790G>A (p.Ser930=)",
"single nucleotide variant", "single nucleotide variant", "single nucleotide variant",
"single nucleotide variant", "single nucleotide variant", "single nucleotide variant",
"HGNC:16369", "HGNC:16369", "HGNC:16369", "HGNC:30213", "HGNC:30213",
"HGNC:30213"), .Dim = 6:5, .Dimnames = list(NULL, c("VarID_build37",
"c.change", "Clinvar_ Name", "Clinvar_ Type", "Clinvar_ HGNC_ID"
)))
结果我想要:
VarID_build37 c.change Clinvar_ Name Clinvar_ Type Clinvar_ HGNC_ID
"chr1:8045045:A:G" "c.501A>G" "NM_007262.5(PARK7):c.501A>G (p.Ala167=)" "single nucleotide variant" "HGNC:16369"
"chr1:8045045:A:G" "c.441A>G"
"chr1:8045045:A:G" "c.414A>G"
"chr1:17314702:C:T" "c.2775G>A"
"chr1:17314702:C:T" "c.2658G>A"
"chr1:17314702:C:T" "c.2790G>A" "NM_022089.4(ATP13A2):c.2790G>A (p.Ser930=)" "single nucleotide variant" "HGNC:30213"
这是基本的R解决方案。(如果愿意,可以替换""
为NA
)。
mydf[,-(1:2)][!apply(mydf,1,function(x) grepl(x["c.change"], x["Clinvar_ Name"])),] <- ""
VarID_build37 c.change Clinvar_ Name Clinvar_ Type Clinvar_ HGNC_ID
[1,] "chr1:8045045:A:G" "c.501A>G" "NM_007262.5(PARK7):c.501A>G (p.Ala167=)" "single nucleotide variant" "HGNC:16369"
[2,] "chr1:8045045:A:G" "c.441A>G" "" "" ""
[3,] "chr1:8045045:A:G" "c.414A>G" "" "" ""
[4,] "chr1:17314702:C:T" "c.2775G>A" "" "" ""
[5,] "chr1:17314702:C:T" "c.2658G>A" "" "" ""
[6,] "chr1:17314702:C:T" "c.2790G>A" "NM_022089.4(ATP13A2):c.2790G>A (p.Ser930=)" "single nucleotide variant" "HGNC:30213"
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