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
strategy for writing out file with lines header initiated with comment sign
4 messages · jim holtman, Rainer M Krug, Mao Jianfeng
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?
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk2lo98ACgkQoYgNqgF2egovxwCeN7G2It+1petLynKW37fIqKbW YIkAmwfMSgfLLZwTGDHJ2dNsVp5muj+7 =Cfj2 -----END PGP SIGNATURE-----
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>:
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk2lo98ACgkQoYgNqgF2egovxwCeN7G2It+1petLynKW37fIqKbW YIkAmwfMSgfLLZwTGDHJ2dNsVp5muj+7 =Cfj2 -----END PGP SIGNATURE-----
Jian-Feng, Mao the Institute of Botany, Chinese Academy of Botany,