[R] Merging two files together in R

john seers (IFR) john.seers at bbsrc.ac.uk
Fri Aug 24 17:00:22 CEST 2007

Try looking at ?merge

If your data is in two dataframes df1 and df2:

merge(df1, df2)

(This will merge on SNPID because that column is common to both


-----Original Message-----
From: r-help-bounces at stat.math.ethz.ch
[mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Morassa Mohseni
Sent: 24 August 2007 15:41
To: r-help at stat.math.ethz.ch
Subject: [R] Merging two files together in R


Thanks in advance for reading this post.

I received some affymetrix genotyping data back recently (250K, Nsp
array)...However, in order for me to do any analysis on this data set, I
need to add append the annotation file to it. Basically I want to do
something that looks like this:

Snpfile(tab delimited):

SNPID  Genotype          X          Y

123       AA                13.4         1.2

456       AB               10.1         12.2

789       BB               2.7            14.4

Annotation file (csv file):

rs#,       SNPID, Chromosome

rs23525,  456,         12

rs78423,  123,          4

rs82342,   789,          9

What I am trying to get is an output file that looks like this:

SNPID  rs#           Chromosome              Genotype          X

123       rs78423      4                                 AA

456       rs23525      12                                AB

789       rs82342       9                                BB

The SNPID is the same in both files so I would like to use that to match
up...but they are not in the same order in both files, so I want to make
sure that I am appending and merging the 2 files correctly. So far all
ive really been able to do is import the files into R...Ive been looking
through the posts, and was wondering if I could use cbind(...) to merge
the files?...not sure though.

Thanks again!!

Morassa Mohseni

PhD Student

Johns Hopkins Dept. of Human Genetics

Baltimore, MD

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