read.csv

?s 11:46 de 16/04/2024, jing hua zhao escreveu:

Dear R-developers,

I came to a somewhat unexpected behaviour of read.csv() which is trivial but worthwhile to note -- my data involves a protein named "1433E" but to save space I drop the quote so it becomes,

Gene,SNP,prot,log10p
YWHAE,13:62129097_C_T,1433E,7.35
YWHAE,4:72617557_T_TA,1433E,7.73

Both read.cv() and readr::read_csv() consider prot(ein) name as (possibly confused by scientific notation) numeric 1433 which only alerts me when I tried to combine data,

all_data <- data.frame()
for (protein in proteins[1:7])
{
     cat(protein,":\n")
     f <- paste0(protein,".csv")
     if(file.exists(f))
     {
       p <- read.csv(f)
       print(p)
       if(nrow(p)>0) all_data  <- bind_rows(all_data,p)
     }
}

proteins[1:7]
[1] "1433B" "1433E" "1433F" "1433G" "1433S" "1433T" "1433Z"

dplyr::bind_rows() failed to work due to incompatible types nevertheless rbind() went ahead without warnings.

Best wishes,


Jing Hua

Hello,

I wrote a file with that content and read it back with


read.csv("filename.csv", as.is = TRUE)


There were no problems, it all worked as expected.