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

[Gundala Viswanath]

Thanks so much Jim,

It works. However how come the "\n" was not removed.
Meaning when I do:

print (x$V3)

it gives something like this:
__OUTPUT__
    [1]  discoidin domain receptor tyrosine kinase 1

    [2]  replication factor C (activator 1) 2, 40kDa

    [3]  heat shock 70kDa protein 6 (HSP70B')

__END__

Note the spacing between the entries. I expect something like:

    [1]  discoidin domain receptor tyrosine kinase 1
    [2]  replication factor C (activator 1) 2, 40kDa
    [3]  heat shock 70kDa protein 6 (HSP70B')
    __END__

Do you have any idea how to fix this?



- Gundala Viswanath
Jakarta - Indonesia


On Mon, Jun 16, 2008 at 10:19 AM, jim holtman <jholtman at gmail.com> wrote:
> 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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>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
>
> --
> Jim Holtman
> Cincinnati, OH
> +1 513 646 9390
>
> What is the problem you are trying to solve?
>