R代码用于分析基因分型数据。

我有这个数据帧（

mydf

）。我需要将列REF和ALT中的字母（DNA字母）与列名称（“A”、“T”、“G”、“C”）匹配，并将相应的数值粘贴在一起作为“REF，ALT”。然而，在TYPE列中有一些行有“snp:+[0-9]”和“flat$”。现在，对于“flat$”行，我想将对应“start”ID的“snp:+[0-9]”中的ALT值相加，并将该ALT值再次粘贴为“REF，ALT”（对于“snp:+[0-9]”和具有相同起始ID的“flat$”，REF值将相同），并获得结果所示的输出。我如何制作一个函数来实现这一点

mydf<-structure(c("chr20:5363934", "chr5:8529759", "chr14:9620689", 
            "chr18:547375", "chr8:5952145", "chr14:8694382", "chr16:2530921", 
            "chr16:2530921", "chr16:2530921", "chr14:4214117", "chr4:7799768", 
            "chr3:9141263", "95", "24", "65", "94", "27", "68", "49", "49", 
            "49", "73", "36", "27", "29", " 1", "49", " 1", "80", "94", "15", 
            "15", "15", "49", "28", "41", "14", "28", "41", "51", "25", "26", 
            "79", "79", "79", "18", " 1", "93", "59", "41", "96", "67", "96", 
            "30", "72", "72", "72", "77", "16", "90", "C", "G", "T", "G", 
            "T", "A", "A", "A", "A", "G", "C", "A", "T", "C", "G", "C", "T", 
            "A", "T", "G", "T", "A", "A", "A", "snp", "snp", "snp", "snp", 
            "snp", "snp", "snp:2530921", "snp:2530921", "snp:flat", "snp", "snp", "snp"), .Dim = c(12L, 
                                                                                   8L), .Dimnames = list(NULL, c("start", "A", "T", "G", "C", "REF", 
                                                                                                                 "ALT", "TYPE")))

---

indx基于
snp[0-9]
的
flat
中值的
sum
不清楚。是否必须是相邻的先前值？是的，总和是对应snp[0-9]的相邻值之和。即。具有相同起始ID的行。对于具有相同起始ID的所有行，ref保持不变，但flat的ALT必须是具有相同起始ID的所有snp的组合（除了flat本身）。是的，它需要更多的工作。我必须更好地对“snp:flat”值进行分组。我在考虑
v1@user277653你能试试我在评论中发布的代码以及
indx吗？我已经更新了答案，并在不同的组合上进行了测试。它与您提供的数据和其他迭代一起工作。如果仍然出现错误，则需要发布不同的示例。因为这些是有效的。这是一种将两个步骤结合为一个步骤的方法。而不是长版本，
x
    start              A    T    G    C    REF ALT TYPE       AD     
 [1,] "chr20:5363934" "95" "29" "14" "59" "C" "T" "snp"      "59,29"
 [2,] "chr5:8529759"  "24" " 1" "28" "41" "G" "C" "snp"      "28,41"
 [3,] "chr14:9620689" "65" "49" "41" "96" "T" "G" "snp"      "49,41"
 [4,] "chr18:547375"  "94" " 1" "51" "67" "G" "C" "snp"      "51,67"
 [5,] "chr8:5952145"  "27" "80" "25" "96" "T" "T" "snp"      "80,80"
 [6,] "chr14:8694382" "68" "94" "26" "30" "A" "A" "snp"      "68,68"
 [7,] "chr16:2530921" "49" "15" "79" "72" "A" "T" "snp:2530921" "49,15"
 [8,] "chr16:2530921" "49" "15" "79" "72" "A" "G" "snp:2530921" "49,79"
 [9,] "chr16:2530921" "49" "15" "79" "72" "A" "T" "snp:flat" "49,94"
[10,] "chr14:4214117" "73" "49" "18" "77" "G" "A" "snp"      "18,73"
[11,] "chr4:7799768"  "36" "28" " 1" "16" "C" "A" "snp"      "16,36"
[12,] "chr3:9141263"  "27" "41" "93" "90" "A" "A" "snp"      "27,27"

indx <- sapply(mydf[,c("REF", "ALT")], function(x) match(x, colnames(mydf)))
flat <- grepl("flat", mydf[,"TYPE"])
x <- `dim<-`(mydf[cbind(rep(1:nrow(mydf), 2), indx)], c(nrow(mydf), 2))
add_ids <- mydf[,"start"][mydf[,"start"] %in% mydf[,"start"][flat] & !flat]
toadd <- x[,2][mydf[,"start"] %in% mydf[,"start"][flat] & !flat]
x[,2][flat] <-tapply(as.numeric(toadd), factor(add_ids, levels=unique(add_ids)), sum)
cbind(mydf, paste(x[,1], x[,2],sep=","))
#       start           A    T    G    C    REF ALT TYPE                 
#  [1,] "chr20:5363934" "95" "29" "14" "59" "C" "T" "snp"         "59,29"
#  [2,] "chr5:8529759"  "24" " 1" "28" "41" "G" "C" "snp"         "28,41"
#  [3,] "chr14:9620689" "65" "49" "41" "96" "T" "G" "snp"         "49,41"
#  [4,] "chr18:547375"  "94" " 1" "51" "67" "G" "C" "snp"         "51,67"
#  [5,] "chr8:5952145"  "27" "80" "25" "96" "T" "T" "snp"         "80,80"
#  [6,] "chr14:8694382" "68" "94" "26" "30" "A" "A" "snp"         "68,68"
#  [7,] "chr16:2530921" "49" "15" "79" "72" "A" "T" "snp:2530921" "49,15"
#  [8,] "chr16:2530921" "49" "15" "79" "72" "A" "G" "snp:2530921" "49,79"
#  [9,] "chr16:2530921" "49" "15" "79" "72" "A" "T" "snp:flat"    "49,94"
# [10,] "chr14:4214117" "73" "49" "18" "77" "G" "A" "snp"         "18,73"
# [11,] "chr4:7799768"  "36" "28" " 1" "16" "C" "A" "snp"         "16,36"
# [12,] "chr3:9141263"  "27" "41" "93" "90" "A" "A" "snp"         "27,27"