[R] [BioC] comparing two tables

[arun]

Hi Tamara,
No problem.
 dat3<- rbind(dat1,dat2)  #Sorry, forgot this line.
A.K.








________________________________
From: Tamara Simakova <tsimakova at sequoiag.com>
To: arun <smartpink111 at 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 <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
>
>
>
>
>
>
>--
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>
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