R gsub column names in all data frames within a list

Question

I have a list of data frames with column names that I want to substitute some strings out, but I can't do it right.

list:
[1]
cpg value.TCGA.06.5415.01A     value.TCGA.02.0003.01A   value.TCGA.16.1062.01A
cg02726808  0.934641544 NA  NA
cg04243127  0.8828403   NA  NA
[2]
cpg value.TCGA.QH.A6CV.01A  value.TCGA.E1.A7Z4.01A  value.TCGA.E1.5303.01A
 cg02726808 0.938556343 0.92163563  0.959269597
 cg04243127 0.886928811 0.842963126 0.937700666
[N]
.....

Desired output:
    list:           
[1]         
cpg 06.5415.01A 02.0003.01A 16.1062.01A
cg02726808  0.934641544 NA  NA
cg04243127  0.8828403   NA  NA
[2]         
cpg QH.A6CV.01A E1.A7Z4.01A E1.5303.01A
cg02726808  0.938556343 0.92163563  0.959269597
cg04243127  0.886928811 0.842963126 0.937700666
[N]         
.....

I tried to write the following:

lapply(lst, function(x) { gsub("value.TCGA.", "", colnames(lst[[x]]))})

Error in R Studio:

Error in llis1[[xy]] : invalid subscript type 'list'
Called from: is.data.frame(x)
Browse[1]> 

And I don't understand what is it about. Thanks for your help.

Answer 1

We can use setNames to replace the column names with the new column names from the sub.

lapply(lst, function(x) setNames(x, sub("value.TCGA.", "", names(x))))

---

Or another option is substring if the 'value.TCGA.' position is the same in all the column names except the first one.

lapply(lst, function(x) setNames(x, c("cpg", substring(names(x)[-1], 12)))

Answer 2

Try

lapply(lst, function(x) {
  colnames(x) <- gsub("value.TCGA.", "", colnames(x))
  return(x)
})

x in this case is an element of lst rather than the index of the element of lst. So in your code, you are trying to do lst[[ lst[[1]] ]]. From here, the error message should make sense.