Mao Jianfeng
2011-Apr-13 10:15 UTC
[R] strategy for writing out file with lines header initiated with comment sign
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
jim holtman
2011-Apr-13 13:15 UTC
[R] strategy for writing out file with lines header initiated with comment sign
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)
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.
>
--
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?