[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 <smartpink111 at 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 <tsimakova at sequoiag.com>
>To: r-help at 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.
>
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