Question

我读了所有'字符串到变量名'的帖子，但没有一个涵盖我的特定问题。我有一个使用seqinr包'read.fasta'制作的载体列表（DNA序列数据）。我有变量的数据框及其位置，我想将数据框中指定位置的列表向量元素转换为其替代值。在个人基础上，这可以使用

完成

list$name[number] <- alternate.character

# I tried
 for (i in 1:length(df$CHROM))
  if (is.na(df$Call[i])) {next} else {get(paste("test$",df$CHROM[i],"[",df$POS[i],"]",sep=""))  <- df$Call[i]}

# example data
 test <- list("One" = c("a","t","a","g","c"),
              "Two" = c("g","a","t","t","a","c","a"))
 df <- data.frame("CHROM"=c(rep("One",2),rep("Two",3)),
             "POS" = c(2,4,1,3,6),
             "REF" = c("t","g","g","t","c"),
             "ALT" = c("a","a","t","g","t"),
             "Call" = c("T","A","G",NA,"T"))

但是'get'会从列表中返回vector元素，并且不允许我将其指定为父列表中的变体。

我想要的是来自

的列表

$One
[1] "a" "t" "a" "g" "c"

$Two
[1] "g" "a" "t" "t" "a" "c" "a"

到

$One
[1] "a" "T" "a" "A" "c"

$Two
[1] "G" "a" "t" "t" "a" "T" "a"

对于测试数据，这不是问题，因为您可以单独执行此操作，但实际数据超过10,000个序列和100,000多个变体。如果您可以对其进行矢量化，则我没有足够的经验来嵌套应用函数，以使其同时处理列表和数据框中的信息。

sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
 [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] seqinr_3.0-7

loaded via a namespace (and not attached):
[1] tools_3.0.2

Answer 1

您可以使用sapply执行此任务：

res <- sapply(names(test), function(x) {
  tmp <- df[df$CHROM == x & !is.na(df$Call), ]
  replace(test[[x]], tmp$POS, as.character(tmp$Call))
})


res
# $One
# [1] "a" "T" "a" "A" "c"
#
# $Two
# [1] "G" "a" "t" "t" "a" "T" "a"

R将字符串转换为变量名称并替换变量

1 个答案: