Hi Tamara, No problem. dat3<- rbind(dat1,dat2) #Sorry, forgot this line. A.K.
________________________________ From: Tamara Simakova <tsimak...@sequoiag.com> To: arun <smartpink...@yahoo.com> Sent: Thursday, May 30, 2013 12:26 PM Subject: Re: [R] [BioC] comparing two tables Hello Arun, Thanks very much for help. Indeed there is a mistake in the resulted table, it should be exactly as in your example. When I use dat3New<-with(dat3,aggregate(info,list(chr,pos,ref,alt),FUN=function(x) x)) colnames(dat3New)<- colnames(dat1) the R returns "dat3 is not found", but with plyr library everything works well. Thank again, Tamara 2013/5/30 arun <smartpink...@yahoo.com> > >Assuming that you wanted to label '1' for table1 and '4' for table2 (info >column). > >Also, not sure why chr2 row is not in the resulted table. > >dat1<- read.table(text=" > >chr pos ref alt >chr1 5 A G >chr1 8 T C >chr2 2 C T >",sep="",header=TRUE,stringsAsFactors=FALSE) > >dat2<-read.table(text=" > >chr pos ref alt >chr1 5 A G >chr1 7 T C >chr1 8 T A >",sep="",header=TRUE,stringsAsFactors=FALSE) >dat1$info<- 1 > dat2$info<-4 > dat3New<-with(dat3,aggregate(info,list(chr,pos,ref,alt),FUN=function(x) x)) > colnames(dat3New)<- colnames(dat1) >dat3New1<-dat3New[order(dat3New$chr,dat3New$pos),] > row.names(dat3New1)<-1:nrow(dat3New1) > dat3New1 ># chr pos ref alt info >#1 chr1 5 A G 1, 4 >#2 chr1 7 T C 4 >#3 chr1 8 T A 4 >#4 chr1 8 T C 1 >#5 chr2 2 C T 1 > >#or >library(plyr) >res<-ddply(merge(dat1,dat2,all=TRUE),.(chr,pos,ref,alt),summarize,info=list(info)) >res ># chr pos ref alt info >#1 chr1 5 A G 1, 4 >#2 chr1 7 T C 4 >#3 chr1 8 T A 4 >#4 chr1 8 T C 1 >#5 chr2 2 C T 1 >names(dat3New1$info)<-NULL > identical(dat3New1,res) >#[1] TRUE > >A.K. > > >----- Original Message ----- >From: tomkina <tsimak...@sequoiag.com> >To: r-help@r-project.org >Cc: >Sent: Thursday, May 30, 2013 4:45 AM >Subject: Re: [R] [BioC] comparing two tables > >Hello, > >I have the similar task. I have two tables and I need to get the third >table containing data from both of them with extra column with information >of what data from which table: > >table1 >chr pos ref alt >chr1 5 A G >chr1 8 T C >chr2 2 C T > >table2 >chr pos ref alt >chr1 5 A G >chr1 7 T C >chr1 8 T A > >resulted table >chr pos ref alt info >chr1 5 A G 1, 4 >chr1 7 T C 4 >chr1 8 T C 1 >chr1 8 T A 4 > >I need all 4 columns (chr, pos, ref and alt) to be compared. I didn't find >this function in Bioconductor. I am a beginner at R and would appreciate any >help. > >Thanks, >Tamara > > > > > > >-- >View this message in context: >http://r.789695.n4.nabble.com/comparing-two-tables-tp3936306p4668272.html >Sent from the R help mailing list archive at Nabble.com. > >______________________________________________ >R-help@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. > > ______________________________________________ R-help@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.
