Undefined columns selected while doing a for loop

August 30, 2022

I have 13 data frames with the same parameters. For each data frame, I want to extract the column P.Value (only the rows which are smaller than 0.05) and add it to a new vector. Instead of writing the same code 13 times, I want to do a for loop:

for (i in (1:13)) {
  
  MyGenes[i] = df[i][df[i]$P.Value < 0.05,]
  
}

I get this error:

Error in `[.data.frame`(df, i) : undefined columns selected

What am I doing wrong? the names of the data frames are df1, df2, df3, and so on. At the end I want MyGenes1, MyGenes2 …. MyGenes13.

>Solution :

You can probably achieve what you want with

for (i in 1:13) {
  
  assign(paste0('MyGenes', i), 
         subset(get(paste0('df', i)), P.Value < 0.05))
}

However, working with a list of data frames (as suggested by wernor) would be more convenient:

# sample data
df.list <- list(data.frame(x=1:5, P.Value=seq(0, .2, length.out=5)),
                data.frame(x=3:7, P.Value=seq(0, .1, length.out=5)))

MyGenes <- lapply(df.list, subset, P.Value < 0.05)