I have 2 files containing data analysed by 2 different methods. I would like to find out which genes appear in both analyses. Can someone show me how to do this? _________________________________________________________________ [[trailing spam removed]] [[alternative HTML version deleted]]
Maybe 'merge', but your message is wa First On 7/26/07, jenny tan <timpanisterwombat@hotmail.com> wrote:> > > > I have 2 files containing data analysed by 2 different methods. I would > like to find out which genes appear in both analyses. Can someone show me > how to do this? > _________________________________________________________________ > [[trailing spam removed]] > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@stat.math.ethz.ch 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. >-- Christophe Pallier (http://www.pallier.org) [[alternative HTML version deleted]]
Maybe with 'merge', but your message is too vague (see http://www.catb.org/~esr/faqs/smart-questions.html). On 7/26/07, jenny tan <timpanisterwombat@hotmail.com> wrote:> > > > I have 2 files containing data analysed by 2 different methods. I would > like to find out which genes appear in both analyses. Can someone show me > how to do this? > _________________________________________________________________ > [[trailing spam removed]] > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@stat.math.ethz.ch 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. >-- Christophe Pallier (http://www.pallier.org) [[alternative HTML version deleted]]
Something like:
# Sample data
g1<-c("gene1", "gene2", "gene3",
"gene4", "gene5", "gene9", "gene10",
"geneA")
g2<-c("gene6", "gene9", "gene1",
"gene2", "gene7", "gene8", "gene9",
"gene1", "gene10")
df1<-cbind(gene=g1, expr=runif(length(g1)))
df2<-cbind(gene=g2, expr=runif(length(g2)))
# Merge
mdf<-merge(df1, df2, by="gene", sort=T)
# Unique list
ug<-unique(mdf[,"gene"])
You may find the "match" command useful and/or the "%in%"
opertaor.
JS
---
-----Original Message-----
From: r-help-bounces at stat.math.ethz.ch
[mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of jenny tan
Sent: 26 July 2007 04:35
To: r-help at stat.math.ethz.ch
Subject: [R] Finding matches in 2 files
I have 2 files containing data analysed by 2 different methods. I would
like to find out which genes appear in both analyses. Can someone show
me how to do this?
_________________________________________________________________
[[trailing spam removed]]
[[alternative HTML version deleted]]
______________________________________________
R-help at stat.math.ethz.ch 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.
Is this what you want?> g1<-c("gene1", "gene2", "gene3", "gene4", "gene5", "gene9", "gene10",+ "geneA")> g2<-c("gene6", "gene9", "gene1", "gene2", "gene7", "gene8", "gene9",+ "gene1", "gene10")> intersect(g1,g2)[1] "gene1" "gene2" "gene9" "gene10" On 7/25/07, jenny tan <timpanisterwombat at hotmail.com> wrote:> > > I have 2 files containing data analysed by 2 different methods. I would like to find out which genes appear in both analyses. Can someone show me how to do this? > _________________________________________________________________ > [[trailing spam removed]] > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at stat.math.ethz.ch 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. >-- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve?