Thank you Stephanie. -Avoks On Thu, Oct 3, 2013 at 8:28 PM, Stephanie M. Gogarten < sdmorris@u.washington.edu> wrote: > Hi Avoks, > > This is more of an R-help question than a Bioconductor question, but > here's something that I think will work for you. Step 1 does some indexing > of your first input file, and step 2 uses the "merge" function in R - see > the man page for that function for more details. > > > f1 <- readLines("f1.txt") > > gene.index <- grep("^GENE", f1) > > snp.index <- grep("^snp", f1) > > end.index <- grep("^END", f1) > > snps <- f1[snp.index] > > genes <- character(length(snps)) > > for (i in 1:length(gene.index)) { > + snps.in.gene <- snp.index > gene.index[i] & snp.index < end.index[i] > + genes[snps.in.gene] <- f1[gene.index[i]] > + } > > snp.by.gene <- data.frame(GENE=genes, SNP=snps, stringsAsFactors=FALSE) > > snp.by.gene > GENE SNP > 1 GENE1 snp001 > 2 GENE1 snp002 > 3 GENE1 snp003 > 4 GENE1 snp004 > 5 GENE2 snp005 > 6 GENE2 snp006 > 7 GENE2 snp007 > 8 GENE2 snp008 > 9 GENE3 snp009 > 10 GENE3 snp010 > 11 GENE3 snp011 > 12 GENE3 snp012 > > f2 <- read.table("f2.txt", as.is=TRUE, header=TRUE) > > f2 > SNP Pval Fst > 1 snp001 5e-04 0.25 > 2 snp002 3e-04 0.75 > 3 snp003 1e-04 0.65 > 4 snp004 1e-05 0.30 > 5 snp005 6e-05 0.50 > 6 snp006 4e-04 0.10 > 7 snp007 3e-05 0.60 > 8 snp008 2e-04 0.75 > > snp.table <- merge(snp.by.gene, f2, by="SNP", all.x=TRUE) > > snp.table > SNP GENE Pval Fst > 1 snp001 GENE1 5e-04 0.25 > 2 snp002 GENE1 3e-04 0.75 > 3 snp003 GENE1 1e-04 0.65 > 4 snp004 GENE1 1e-05 0.30 > 5 snp005 GENE2 6e-05 0.50 > 6 snp006 GENE2 4e-04 0.10 > 7 snp007 GENE2 3e-05 0.60 > 8 snp008 GENE2 2e-04 0.75 > 9 snp009 GENE3 NA NA > 10 snp010 GENE3 NA NA > 11 snp011 GENE3 NA NA > 12 snp012 GENE3 NA NA > > Stephanie > > > On 10/3/13 12:23 AM, Ovokeraye Achinike-Oduaran wrote: > >> Hi all, >> >> I have two files I need to merge but first I need to reformat one of >> them...it looks like this: >> >> GENE1 >> snp001 >> snp002 >> snp003 >> snp004 >> >> END >> GENE2 >> snp005 >> snp006 >> snp007 >> snp008 >> >> END >> >> GENE3 >> snp009 >> snp010 >> snp011 >> snp012 >> >> END >> >> It's pretty much a set file from Plink. What I'd like to do is to have the >> file looking like this: >> >> GENE1 snp001 >> GENE1 snp002 >> GENE1 snp003 >> GENE1 snp004 >> GENE2 snp005 >> GENE2 snp006 >> GENE2 snp007 >> GENE2 snp008 >> GENE3 snp009 >> GENE3 snp010 >> ... >> >> The second file looks pretty much a file with most of the same SNPs for >> the >> most part but with additional data so I pretty much want to do something >> like can be done on Microsoft Access merging the two files using the >> common >> unique identifier the snps. >> >> SNP >> Pval Fst snp001 0.0005 0.25 snp002 0.0003 0.75 snp003 0.0001 0.65 >> snp004 >> 0.00001 0.3 snp005 0.00006 0.5 snp006 0.0004 0.1 snp007 0.00003 0.6 >> snp008 0.0002 0.75 >> >> Any help with this in R will be greatly appreciated. >> >> Thanks. >> >> Avoks >> >> [[alternative HTML version deleted]] >> >> >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> >> [[alternative HTML version deleted]]