[R] Crosstabs in R

[Tan Hui Hui Jenny]

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