Re: [R] Crosstabs in R

From: Jim Brennan <jfbrennan_at_rogers.com>
Date: Tue 28 Jun 2005 - 12:25:55 EST


Here is one way to do it.
> jen2<-reshape(jen,idvar="DNA",timevar="center",direction="wide")
This makes it easier to work with.

> jen2<-replace(jen2,jen2=="?",NA)

Change the question marks to NA.

> jen2$match1<-((jen2[,2]==jen2[,4])*1)
> jen2$match2<-((jen2[,3]==jen2[,5])*1)
> jen2

      DNA snp1.1 snp2.1 snp1.2 snp2.2 match1 match2
1 NA07019      A      A      A      A      1      1
2 NA07348      M      G      M      G      1      1
3 NA10830      A      G      A      G      1      1
4 NA10851      M      G      M      G      1      1
5 NA10857      A      G      A      G      1      1
6 NA10860      A      G      A      G      1      1
7 NA10861      A      G      A      G      1      1
8 NA12761   <NA>      R      A      A     NA      0

> mean(jen2[,6:7])

match1 match2

    NA 0.875
> mean(jen2[,6:7],na.rm=T)

match1 match2
 1.000 0.875
>

-----Original Message-----
From: r-help-bounces@stat.math.ethz.ch
[mailto:r-help-bounces@stat.math.ethz.ch] On Behalf Of Tan Hui Hui Jenny Sent: June 27, 2005 9:13 PM
To: r-help@stat.math.ethz.ch

Subject: [R] Crosstabs in R

HI,

        I have the data in the following format. My aim is to determine the concordance in genotype calls (SNP1, 2, 3,etc) at two centers.          

	DNA center snp1 snp2
	NA07019 1 A A
	NA07348 1 M G
	NA10830 1 A G
	NA10851 1 M G
	NA10857 1 A G
	NA10860 1 A G
	NA10861 1 A G
	NA12761 1 ? R
	NA07019 2 A A
	NA07348 2 M G
	NA10830 2 A G
	NA10851 2 M G
	NA10857 2 A G
	NA10860 2 A G
	NA10861 2 A G
	NA12761 2 A A
	 
	In SPSS, I would create individual crosstabulation tables and any
positive integer values (counts) falling outside of the diagonal are disagreements in calls by the 2 centers (SNP2).

        At SNP1, there are total of 7 genotype counts to compare (one DNA did not have genotype readout). And 7/7 are in agreement.          

        At SNP2, all 8 DNA samples were successfully typed by both centers. There is one discrepant call between centers.

        Q1: how do I create the same crosstabs in R?          

        Eventually, I would summarize the data as follows:          

	SNP N_to_compare N_agreement %Concordance
	snp1 7  7  100
	snp2 8  7  87.5
	etc
	 
	Q2: From the individual crosstabs tables, can I automatically
extract those numbers in columns 2 and 3?                    
	rgds,
	jenny

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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 Received on Tue Jun 28 12:38:04 2005

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