sm.compare {snpStats} | R Documentation

## Compare two SnpMatrix objects

### Description

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

### Usage

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

### Arguments

`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

### Details

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.

### Value

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`

### Note

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

### Author(s)

David Clayton dc208@cam.ac.uk

### See Also

`SnpMatrix-class`, `XSnpMatrix-class`

### Examples

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    ## No example yet available
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[Package snpStats version 1.40.0 Index]