Re: [R] strategy for writing out file with lines header initiated with comment sign

From: Mao Jianfeng <jianfeng.mao_at_gmail.com>
Date: Wed, 13 Apr 2011 15:34:41 +0200

Dear Jim and Rainer,

I learned much from you all. It is my first time to experience the functions, like file(), writeLines(), close().

Thanks a lot.

Best,

Jian-Feng,

2011/4/13 Rainer M Krug <r.m.krug_at_gmail.com>:
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> On 13/04/11 15:15, jim holtman wrote:
>> Here is an outline of how to do it using connections:
>>
>> con <- file('/temp/mytemp.txt', 'w')
>> writeLines(c("#comment", "# lines", "# in the file"), con = con)
>> # create some data to be output as 'tab' separated
>> myData <- as.data.frame(matrix(letters[1:25], 5))
>> write.table(myData, file = con, sep = '\t')
>> close(con)
>> con <- file('/temp/mytemp.txt', 'w')
>> writeLines(c("#comment", "# lines", "# in the file"), con = con)
>> # create some data to be output as 'tab' separated
>> myData <- as.data.frame(matrix(letters[1:25], 5))
>> write.table(myData, file = con, sep = '\t')
>> close(con)
>
> or:
>
> myData <- as.data.frame(matrix(letters[1:25], 5))
> writeLines(c("#comment", "# lines", "# in the file"), con = "./test.csv")
> write.table(myData, "./test.csv", append=TRUE)
>
> Cheers,
>
> Rainer
>
>>
>>
>>
>> On Wed, Apr 13, 2011 at 6:15 AM, Mao Jianfeng <jianfeng.mao_at_gmail.com> wrote:
>>> Dear all,
>>>
>>> I have data.frame object in R. I want to export it in tab-delimited
>>> file with several lines of header initiated with comment sign (#). I
>>> do not know how to do that in R. Could you please give helps on this
>>> problem?
>>>
>>> Thanks in advance.
>>>
>>> Best,
>>> Jian-Feng,
>>>
>>> ##################################################################
>>> The lines I want to write in the header lines look like, with words in
>>> the last line (here the line "#CHROM POS     ID        REF ALT    QUAL
>>> FILTER INFO                              FORMAT      NA00001") be
>>> separated by tab :
>>>
>>>
>>> ##fileformat=VCFv4.1
>>> ##fileDate=20090805
>>> ##source=myImputationProgramV3.1
>>> ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
>>> ##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo
>>> sapiens",taxonomy=x>
>>> ##phasing=partial
>>> ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
>>> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
>>> ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
>>> ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
>>> ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
>>> ##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
>>> ##FILTER=<ID=q10,Description="Quality below 10">
>>> ##FILTER=<ID=s50,Description="Less than 50% of samples have data">
>>> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
>>> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
>>> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
>>> ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
>>> #CHROM POS     ID        REF ALT    QUAL FILTER INFO
>>>           FORMAT      NA00001
>>>
>>> ______________________________________________
>>> R-help_at_r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>>
>>
>
>
> - --
> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
> Biology, UCT), Dipl. Phys. (Germany)
>
> Centre of Excellence for Invasion Biology
> Stellenbosch University
> South Africa
>
> Tel :       +33 - (0)9 53 10 27 44
> Cell:       +33 - (0)6 85 62 59 98
> Fax :       +33 - (0)9 58 10 27 44
>
> Fax (D):    +49 - (0)3 21 21 25 22 44
>
> email:      Rainer_at_krugs.de
>
> Skype:      RMkrug
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-- 
Jian-Feng, Mao

the Institute of Botany,
Chinese Academy of Botany,

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