[英]Expand loop over multiple columns in R
我有一個表(mydf),如下所示。 我想將其用於R中的循環(我的代碼),該循環僅適用於一列(本例中為ALT1列),以遍歷所有包含ALT1到ALTn的列,並將輸出存儲在final1到finaln的單獨變量中。 目的是在ALT1到ALTn之間循環以匹配核苷酸列(A,C,G,T,N)並獲得相應的值,如下結果所示。感謝您的幫助!
我的代碼
final1 <- {}
i <- 1
result =merge(coverage.bam, rows.concat.alt, by="start")
for(i in 1:nrow(result)){
final1[i] = paste(paste(result$chr[i], result$start[i], result$end[i],sep=":"),"-",
result$REF[i],"(",result[,(as.character(result$REF[i]))][i],")",",", result$ALT1[i],
"(",result[,(as.character(result$ALT1[i]))][i][!is.na(result[,(as.character(result$ALT1[i]))][i])],")",sep="")
}
final1
我試圖通過ALTn擴展ALT的代碼,但是它不起作用,您能幫我解決這個問題嗎?
final <- list()
setValue<-function(element){
print(element)
for(i in 1:nrow(result)){
final[[i]] = paste(paste(result$chr[i], result$start[i], result$end[i],sep=":"),"-",
result$REF[i],"(",result[,(as.character(result$REF[i]))][i],")",",", result[,element][i],
"(",result[,(as.character(result[,element][i])))][i][!is.na(result[,(as.character(result[,element][i])][i])],")",sep="")
}
}
for(i in colnames(result)){
if(grepl('ALT', i)){
setValue(i)
}
}
mydf
chr start end A C G T N = - REF ALT ALT1 ALT2 ALT3 ALTn
1 chr10 102022031 102022031 NA 34 NA NA NA NA NA C G G NA NA NA
2 chr10 102220574 102220574 2 22 2 3 NA NA NA C AGT A G T NA
3 chr10 115322228 115322228 NA 25 NA NA NA NA NA C A A NA NA NA
4 chr10 122222925 122222925 30 NA NA NA NA NA NA A C C NA NA NA
5 chr10 121111042 121111042 NA 48 NA NA NA NA NA C T T NA NA NA
6 chr10 124444484 124444484 NA 60 NA NA NA NA NA C T T NA NA NA
結果
"chr10:102022031:102022031-C(34),G()" "chr10:102220574:102220574-C(22),A(2),G(2),T(3)" "chr10:115322228:115322228-C(25),A()"
[4] "chr10:122222925:122222925-A(30),C()" "chr10:121111042:121111042-C(48),T()" "chr10:124444484:124444484-C(60),T()"
嘗試
p1 <- do.call(paste,c(mydf[1:3], sep=":"))
p2 <- apply(mydf[c(4:8, 11:16)], 1, function(x) {
Un1 <- unique(match( x[7:11], names(x)[1:4], nomatch=0))
i1 <- match(x[6], names(x))
v1 <- paste0(names(x[i1]),'(', x[i1], ')')
v2 <- as.numeric(x[Un1])
v2[is.na(v2)] <- ''
v3 <-paste(names(x[Un1]), '(', v2, ')', sep='', collapse=",")
paste(v1, v3, sep=",") })
paste(p1, p2, sep="-")
#[1] "chr10:102022031:102022031-C(34),G()"
#[2] "chr10:102220574:102220574-C(22),A(2),G(2),T(3)"
#[3] "chr10:115322228:115322228-C(25),A()"
#[4] "chr10:122222925:122222925-A(30),C()"
#[5] "chr10:121111042:121111042-C(48),T()"
#[6] "chr10:124444484:124444484-C(60),T()"
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