regex - How to rename a column of a data frame with part of the data frame identifier in R?

Question

I've got a number of files that contain gene expression data. In each file, the gene name is kept in a column "Gene_symbol" and the expression measure (a real number) is kept in a column "RPKM". The file name consists of an identifier followed by _ and the rest of the name (ends with "expression.txt"). I would like to load all of these files into R as data frames, for each data frame rename the column "RPKM" with the identifier of the original file and then join the data frames by "Gene_symbol" into one large data frame with one column "Gene_symbol" followed by all the columns with the expression measures from the individual files, each labeled with the original identifier.

I've managed to transfer the identifier of the original files to the names of the individual data frames as follows.

files <- list.files(pattern = "expression.txt$")
for (i in files) {var_name = paste("Data", strsplit(i, "_")[[1]][1], sep = "_"); assign(var_name, read.table(i, header=TRUE)[,c("Gene_symbol", "RPKM")])}

So now I'm at a stage where I have dataframes as follows:

Data_id0001 <- data.frame(Gene_symbol=c("geneA","geneB","geneC"),RPKM=c(2.43,5.24,6.53))
Data_id0002 <- data.frame(Gene_symbol=c("geneA","geneB","geneC"),RPKM=c(4.53,1.07,2.44))

But then I don't seem to be able to rename the RPKM column with the id000x bit. (That is in a fully automated way of course, looping through all the data frames I will generate in the real scenario.)

I've tried to store the identifier bit as a comment with the data frames but seem to be unable to assign the comment from within a loop.

Any help would be appreciated,

mce

Answer 1

You should never work this way in R. You should always try keeping all your data frames in a list and operate over them using function such as lapply etc. Thus, instead of using assign, just create an empty list of length of your files list and fill it with the for loop

For your current situation, we can fixed it using ls and mget combination in order to pull this data frames from the global environment into a list and then change the columns of interest.

temp <- mget(ls(pattern = "Data_id\d+$"))
lapply(names(temp), function(x) names(temp[[x]])[2] <<- gsub("Data_", "", x))
temp
#$Data_id0001
#   Gene_symbol id0001
# 1       geneA   2.43
# 2       geneB   5.24
# 3       geneC   6.53
# 
# $Data_id0002
#   Gene_symbol id0002
# 1       geneA   4.53
# 2       geneB   1.07
# 3       geneC   2.44

You could eventually use list2env in order to get them back to the global environment, but you should use with caution