[R] [BioC] comparing two tables

[arun]

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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