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

最新推荐文章于 2024-07-20 09:40:13 发布

土豆西红柿青椒

最新推荐文章于 2024-07-20 09:40:13 发布

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分类专栏：报错文章标签：生物信息学

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本文介绍了解决使用read_delim函数读取文件时出现的解析错误问题，特别是当第三列被误判为logical类型时的解决方案。通过调整guess_max参数的值，确保了数据的正确读取。

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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