Thanks much for your help! This almost works. However, now I am getting the
following error:
> for(i in all.files) {
+ if (i==all.files[1]) new.data <- read.table(i,header=TRUE) else {
+ new.data <- rbind(new.data, read.table(i))}}
Error in match.names(clabs, names(xi)) :
names do not match previous names
I am wondering if this is because R adds row numbers as a numerical column to
the table of the first file it reads?
________________________________________
From: Weidong Gu [anopheles...@gmail.com]
Sent: Tuesday, August 30, 2011 12:00 PM
To: Vining, Kelly
Cc: r-help@r-project.org
Subject: Re: [R] column names with rbind loop
How about to add a conditional statement to get the header from 1st file
for(i in all.files) {
if (i==all.files[1]) new.data <- read.table(i,header=TRUE) else {
new.data <- rbind(new.data, read.table(i))}}
Weidong Gu
On Tue, Aug 30, 2011 at 1:42 PM, Vining, Kelly
<kelly.vin...@oregonstate.edu> wrote:
> Hello R users.
>
> This is a fairly basic question:
>
> I am concatenating data from sets of files in a directory using a loop. The
> column names in all files are exactly the same. My understanding is that
> rbind takes column names from the first file it reads. However, my output is
> showing that the column names are treated as a first data row, not treated as
> headers.
>
> I compile my file names like this:
>
>> all.files <- list.files()
>> all.files
> [1] "1.rpkm" "10.rpkm" "11.rpkm" "12.rpkm" "13.rpkm" "14.rpkm"
> [7] "15.rpkm" "16.rpkm" "17.rpkm" "18.rpkm" "19.rpkm" "2.rpkm"
> [13] "3.rpkm" "4.rpkm" "5.rpkm" "6.rpkm" "7.rpkm" "8.rpkm"
> [19] "9.rpkm"
>
> Then loop through them like this:
>> new.data <- NULL
>> for(i in all.files) {
> + in.data <- read.table(i)
> + new.data <- rbind(new.data, in.data)}
>> head(new.data)
> V1 V2 V3 V4 V5 V6 V7
> 1 seq_id source type start end score strand
> 2 scaffold_1 Ptrichocarpav2_0 gene_body 12639 13384 . +
> 3 scaffold_1 Ptrichocarpav2_0 gene_body 22190 22516 . +
> 4 scaffold_1 Ptrichocarpav2_0 gene_body 74076 75893 . +
> 5 scaffold_1 Ptrichocarpav2_0 gene_body 80207 81289 . -
> 6 scaffold_1 Ptrichocarpav2_0 gene_body 105236 107712 . +
>
>
> As you can see, R is putting a "V1, V2..." header row here because I didn't
> say "header=TRUE" in my read.table command. But if I do this within the loop,
> I get an error. If I try to delete the V1, V2 row after the fact by
>
> new.data <- new.data[-1,]
>
> R deletes my "real" header row.
>
> How can I get the header that I want?
>
> Thanks for any help,
> --Kelly V.
>
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>
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