read_delim 报错解决 “Warning: 754 parsing failures.”

灰太狼 2022-11-05 10:50 312阅读 0赞 
  1. 报错信息如下：
  3. Parsed with column specification:
  4. cols(
  5.   ECs = col_character(),
  6.   Combine_IDs = col_character(),
  7.   compoundIDs = col_logical()
  8. )
  9. Warning: 754 parsing failures.
  10.  row         col           expected                                                                                                                                                                                                   actual                                                                                                                                                                                   file
  11. 3257 compoundIDs 1/0/T/F/TRUE/FALSE CID:942,                                                                      '3241_healthy_microbiome_compoundsID.txt'
  12. 3258 compoundIDs 1/0/T/F/TRUE/FALSE CID [... truncated]

根据信息定位到是read_delim读入报的错 

  1. individuals_microbiome_combined_enzyme <- read_delim( "3214_healthy_microbiome_compoundsID.txt", sep = ""), 
  2.                                                        delim = "\t") %>%
  4. separate_rows(., compoundIDs, sep = ",")

根据报错信息，read_delim把我的文件第三列判断为logical数据，这才导致后面读入报错。

因为read_delim是根据文件前几列来猜测数据结构，因为我有些行是空值，而有数值的又在后面，所以只需要把guess的行数提高些就可以了，这样第三列就会读入character了

  1. individuals_microbiome_combined_enzyme <- read_delim( "3214_healthy_microbiome_compoundsID.txt", sep = ""), 
  2.                                                        delim = "\t", guess_max = 50000) %>%
  4. separate_rows(., compoundIDs, sep = ",")

输出信息

  1. Parsed with column specification:
  2. cols(
  3.   ECs = col_character(),
  4.   Combine_IDs = col_character(),
  5.   compoundIDs = col_character()

参考Ref:

https://cran.r-project.org/web/packages/readr/vignettes/readr.html

发表评论

表情：
评论列表 （有 0 条评论，312人围观）

还没有评论，来说两句吧...

相关阅读