Question

我有一个字符向量列表，我想将列表写入包含所有字符向量的单个文件。以下是我需要的一个例子：

>str(mylist)
List of 19
$ geneset1    : chr [1:140] "ASGR2" "ATXN7L3" "BCL6B" "C6orf211" ...
$ geneset2    : chr [1:174] "CKS1B" "CREBL2" "CTNNB1" "CTTN" ...
$ geneset3    : chr [1:346] "AGTR1" "C6" "C6orf211" "CCNK" ...
$ geneset4    : chr [1:259] "ASGR2" "ATF7IP" "ATXN7L3" "CKS1B" ...

我想要的输出是这样的文件：

#myfile
>geneset1
ASGR2 ATXN7L3 BCL6B C6orf211
>geneset2
ASGR2 ATXN7L3 BCL6B C6orf211
>geneset3
AGTR1 C6 C6orf211 CCNK

我的方法是：

writeLines(unlist(lapply(mylist, FUN=function(x)paste(x, collapse=" "))), con="test.txt")

但是，我不知道如何添加“＆gt;”在行的开头

由于

Answer 1

你可以使用for looop：

out=stdout()

X <- list(geneset1= c("ASGR2","ATXN7L3","BCL6B","C6orf211"),
          geneset2= c("CKS1B","CREBL2","CTNNB1","CTTN"),
          geneset3= c("AGTR1","C6","C6orf211","CCNK" ),
          geneset4= c("ASGR2","ATF7IP","ATXN7L3","CKS1B" ) )

for(i in names(X)) {
    cat(">", i, "\n", file=out)
    cat(X[[i]], "\n", file=out)
}

Answer 2

足够接近，

writeLines(sapply(names(X),function(x) paste(paste0(">",x,"\n"),paste(X[[x]],collapse=" "))), con="test.txt")

Answer 3

一种方法是使用use.names中的unlist参数，然后使用paste或paste0附加名称：

mylist <- list(geneset1 = c("ASGR2","ATXN7L3","BCL6B","C6orf211"),
               geneset2 = c("CKS1B","CREBL2","CTNNB1","CTTN"),
               geneset3 = c("AGTR1","C6","C6orf211","CCNK" ),
               geneset4 = c("ASGR2","ATF7IP","ATXN7L3","CKS1B" ) )

unlisted <- unlist(lapply(mylist, function(x) { paste(x, collapse = " ") }), use.names = TRUE)
names(unlisted) <- paste0(">", names(unlisted))
names(unlisted)

write.table(unlisted, file = "test.txt", quote = FALSE, 
            sep = "\n", col.names = FALSE)

Answer 4

将Neal的解决方案变成一个功能：

writeGeneSets <- function(genesets, filename) {
    if (missing(filename)) {
        conn <- stdout()
    } else {
        conn <- file(filename, open="w")
        on.exit( close(conn) )
    }

    for (name in names(genesets)) {
        writeLines(paste(">", name), conn)
        writeLines(paste(genesets[[name]], collapse=" "), conn)
    }
}

......我们可以这样试试：

genesets <- list(geneset1= c("ASGR2","ATXN7L3","BCL6B","C6orf211"),
                 geneset2= c("CKS1B","CREBL2","CTNNB1","CTTN"),
                 geneset3= c("AGTR1","C6","C6orf211","CCNK" ),
                 geneset4= c("ASGR2","ATF7IP","ATXN7L3","CKS1B" ) )
writeGeneSets(genesets)
writeGeneSets(genesets, "test1.txt")

将字符向量列表写入R

4 个答案: