R help - Aug 2011 - column names with rbind loop

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.

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.Vining at 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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