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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