sm.compare: Compare two SnpMatrix objects
In snpStats: SnpMatrix and XSnpMatrix classes and methods

Description Usage Arguments Details Value Note Author(s) See Also Examples

For quality control purposes, it is sometimes necessary to compare genotype data derived from different sources. This function facilitates this.

1	sm.compare(obj1, obj2, row.wise = TRUE, col.wise = TRUE)

`obj1`	The first of the two `SnpMatrix` objects to be compared
`obj2`	The second `SnpMatrix` object
`row.wise`	Calculate comparison statistics aggregated in a row-wise manner
`col.wise`	Calculate column-wise comparison statistics

Initially row and column names of the two objects are compared to identify subsets of subjects and SNPs which they have in common. Then, every instance of a SNP genotype in the two objects are compared and agreements and disagreements counted by row and/or by column.

If only one of the row-wise and column-wise summaries are to be calculated, the return value is a matrix with rows defined by subjects or SNPs and columns giving counts of:

`Agree`	Agreements (all)
`Disagree`	Disgreements (all)
`NA.agree`	Genotype coded `NA` in both objects
`NA.disagree`	Genotype coded `NA` in only one object
`Hom.agree`	Objects agree and genotype is homozygous
`Hom.switch`	Genotype coded as homozygous in both objects, but alleles switched
`Het.agree`	Genotype coded as heterozygous in both objects
`Het.Hom`	Genotype coded as heterozygous in one object and homozygous in the other

If both row-wise and column-wise summaries are computed (the default behaviour) , the function returns a list containing two matrices of the form described above. These are named row.wise and col.wise

No special provision is yet made for objects of class XSnpMatrix, in which haploid calls are coded as homozygous.

David Clayton dc208@cam.ac.uk

SnpMatrix-class, XSnpMatrix-class