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
--
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