`$<-.data.frame`(`*tmp*`, tagValueCELL, value = character(0)) : replacement has 0 rows, data has 22204

Question

我正在使用以下代码。

1.clones.tsv

的文件有

22204

行。

read_mixcr_n_trans<- function(file,...){
  df <- read.delim(file)
  # transform the cell id {be consist with RNA data}
  {
    well<- gsub(df$cellId,pattern = "[AGCT]*-",replacement = "")
    hp<- gsub(df$cellId,pattern = "-[AGCT]*-.*",replacement = "")
    rt<- str_extract(df$cellId,pattern = "-[AGCT]{10}")%>%
      str_sub(.,start = 2,end = nchar(.))
  }
  # add a column named "tagValueCELL"  {as normal mixcr output}
  df$tagValueCELL<- paste(well,hp,rt,sep ="_" )
  return(df)
}

fn1 <- "1.clones.tsv"

filelist <- c(fn1)
samples <- c("A")

contig_list<- lapply(filelist, function(x) read_mixcr_n_trans(x))

Error in `$<-.data.frame`(`*tmp*`, tagValueCELL, value = character(0)) :
replacement has 0 rows, data has 22204

回溯

7.
stop(sprintf(ngettext(N, "replacement has %d row, data has %d",
"replacement has %d rows, data has %d"), N, nrows), domain = NA)
6.
`$<-.data.frame`(`*tmp*`, tagValueCELL, value = character(0))
5.
`$<-`(`*tmp*`, tagValueCELL, value = character(0))
4.
read_mixcr_n_trans(x)
3.
FUN(X[[i]], ...)
2.
lapply(filelist, function(x) read_mixcr_n_trans(x))
1.
lapply(filelist, function(x) read_mixcr_n_trans(x))

调试

function (x, name, value) 
{
  cl <- oldClass(x)
  class(x) <- NULL
  nrows <- .row_names_info(x, 2L)
  if (!is.null(value)) {
    N <- NROW(value)
    if (N > nrows) 
      stop(sprintf(ngettext(N, "replacement has %d row, data has %d", 
        "replacement has %d rows, data has %d"), N, 
        nrows), domain = NA)
    if (N < nrows) 
      if (N > 0L && (nrows%%N == 0L) && length(dim(value)) <= 
        1L) 
        value <- rep(value, length.out = nrows)
      else stop(sprintf(ngettext(N, "replacement has %d row, data has %d", 
        "replacement has %d rows, data has %d"), N, 
        nrows), domain = NA)
    if (is.atomic(value) && !is.null(names(value))) 
      names(value) <- NULL
  }```

`Debug location is approximate because the source is not available`

Answer 1

well<- gsub(df$cellId,pattern = "[AGCT]*-",replacement = "")
    hp<- gsub(df$cellId,pattern = "-[AGCT]*-.*",replacement = "")
    rt<- str_extract(df$cellId,pattern = "-[AGCT]{10}")%>%

将“cellID”更改为“tagValueCELL”

read_mixcr_n_trans<- function(file,...){
  df <- read.delim(file)
  # transform the cell id {be consist with RNA data}
  {
    well<- gsub(df$tagValueCELL,pattern = "[AGCT]*-",replacement = "")
    hp<- gsub(df$tagValueCELL,pattern = "-[AGCT]*-.*",replacement = "")
    rt<- str_extract(df$tagValueCELL,pattern = "-[AGCT]{10}")%>%
      str_sub(.,start = 2,end = nchar(.))
  }
  # add a column named "tagValueCELL"  {as normal mixcr output}
  df$tagValueCELL<- paste(well,hp,rt,sep ="_" )
  return(df)
}

fn1 <- "36.clones.tsv"
filelist <- c(fn1)
samples <- c("A")
contig_list<- lapply(filelist, function(x) read_mixcr_n_trans(x))