r - fread 无法将裸露的 + 或 - 识别为字符字段

Question

我正在尝试 fread 一些看起来像这样并且大小约为 2GB 的文件:

head file.bed
chr1    19922471        19924471        +       NM_001204088    tss     1       0
chr1    19922471        19924471        +       NM_001204088    tss     2       0
chr1    19922471        19924471        +       NM_001204088    tss     3       0
chr1    19922471        19924471        +       NM_001204088    tss     4       0
chr1    19922471        19924471        +       NM_001204088    tss     5       0
chr1    19922471        19924471        +       NM_001204088    tss     6       0
chr1    19922471        19924471        +       NM_001204088    tss     7       0
chr1    19922471        19924471        +       NM_001204088    tss     8       0
chr1    19922471        19924471        +       NM_001204088    tss     9       0
chr1    19922471        19924471        +       NM_001204088    tss     10      0

第 4 列也有类似数量的“-”。在 R 中读取 +/- 变成 0:

cov.data <- fread(file)
head(cov.data)
     V1       V2       V3 V4           V5  V6 V7 V8
1: chr1 19922471 19924471  0 NM_001204088 tss  1  1
2: chr1 19922471 19924471  0 NM_001204088 tss  2  1
3: chr1 19922471 19924471  0 NM_001204088 tss  3  1
4: chr1 19922471 19924471  0 NM_001204088 tss  4  1
5: chr1 19922471 19924471  0 NM_001204088 tss  5  1
6: chr1 19922471 19924471  0 NM_001204088 tss  6  0

我查看了文档，但没有弄清楚原因。有什么建议么？由于 fread 仍在开发中，这可能是一个错误吗？

Answer 1

两件事:

首先，如果您的文件带有引号，也就是说，如果您的 strand 列是 "+" 或 "-"，然后 data.table 版本 1.8.8 中的 fread 将正确读取。

第二，this has been rectified in data.table version 1.8.9 ，您可以使用以下方式安装:

install.packages("data.table",repos="http://R-Forge.R-project.org", type="source")

如果需要，你可以安装devtools 然后使用dev_mode(TRUE) 进入开发模式然后安装data.table这样就不会影响你正常运行data.table 1.8.8.

从 1.8.9 复制/粘贴相关变更日志:

NEW FEATURES
o  fread :
   * If some column names are blank they are now given default names rather than causing
       the header row to be read as a data row. Thanks to Simon Judes for suggesting.

   * "+" and "-" are now read as character rather than integer 0. Thanks to Alvaro Gonzalez for reporting.
   https://stackoverflow.com/questions/15388714/reading-strand-column-with-fread-data-table-package

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