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

灰太狼 2022-11-05 10:50 219阅读 0赞

报错信息如下：

Parsed with column specification:
    cols(
      ECs = col_character(),
      Combine_IDs = col_character(),
      compoundIDs = col_logical()
    )
    Warning: 754 parsing failures.
     row         col           expected                                                                                                                                                                                                   actual                                                                                                                                                                                   file
    3257 compoundIDs 1/0/T/F/TRUE/FALSE CID:942,                                                                      '3241_healthy_microbiome_compoundsID.txt'
    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

individuals_microbiome_combined_enzyme <- read_delim( "3214_healthy_microbiome_compoundsID.txt", sep = ""), 
                                                           delim = "\t") %>%
    
    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

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

输出信息

Parsed with column specification:
    cols(
      ECs = col_character(),
      Combine_IDs = col_character(),
      compoundIDs = col_character()

参考Ref:

[https://cran.r-project.org/web/packages/readr/vignettes/readr.html][https_cran.r-project.org_web_packages_readr_vignettes_readr.html]

[https_cran.r-project.org_web_packages_readr_vignettes_readr.html]: https://cran.r-project.org/web/packages/readr/vignettes/readr.html