[R] Separator with " | " for read.table

[jim holtman]

Does this give you what you want:

> x <- read.table(textConnection("#GDS_ID GENE_NAME GENE_DESCRIPTION GENE_FUNCTION
+ 1007_s_at | DDR1 | discoidin domain receptor tyrosine kinase 1 |
protein-coding
+ 1053_at | RFC2 | replication factor C (activator 1) 2, 40kDa | protein-coding
+ 117_at | HSPA6 | heat shock 70kDa protein 6 (HSP70B') |
protein-coding"), sep="|", quote='')
> closeAllConnections()
>
> x
          V1      V2                                            V3
         V4
1 1007_s_at    DDR1   discoidin domain receptor tyrosine kinase 1
protein-coding
2   1053_at    RFC2   replication factor C (activator 1) 2, 40kDa
protein-coding
3    117_at   HSPA6          heat shock 70kDa protein 6 (HSP70B')
protein-coding
>


You had a quote(') in your data; you need to have quote='' in the read.table.

On Sun, Jun 15, 2008 at 9:11 PM, Gundala Viswanath <gundalav at gmail.com> wrote:
> Hi,
>
> I have the following data file to be parsed and captured as a data frame:
>
> __DATA__
> #GDS_ID GENE_NAME GENE_DESCRIPTION GENE_FUNCTION
> 1007_s_at | DDR1 | discoidin domain receptor tyrosine kinase 1 | protein-coding
> 1053_at | RFC2 | replication factor C (activator 1) 2, 40kDa | protein-coding
> 117_at | HSPA6 | heat shock 70kDa protein 6 (HSP70B') | protein-coding
>
> __END__
>
> In particular it is separated by " | " , namely - space, bar, space.
> However I tried this without avail:
>
> geneinfo <- read.table("mydata.txt", sep=" | ", comment.char="\#")
> print(geneinfo)
>
> I also tried with sep= "|", it gave a wrong parsing. Please advice.
>
> - Gundala Viswanath
> Jakarta - Indonesia
>
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>



-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem you are trying to solve?