From: Jim Brennan <jfbrennan_at_rogers.com>

Date: Tue 28 Jun 2005 - 12:25:55 EST

*> mean(jen2[,6:7])
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match1 match2

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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

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")
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This makes it easier to work with.

*> jen2<-replace(jen2,jen2=="?",NA)
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Change the question marks to NA.

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

match1 match2

NA 0.875

*> mean(jen2[,6:7],na.rm=T)
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match1 match2

1.000 0.875

*>
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-----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 anypositive 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 automaticallyextract those numbers in columns 2 and 3?

rgds, jenny ______________________________________________R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide!

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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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