sm.compare: Compare two SnpMatrix objects

In snpStats: SnpMatrix and XSnpMatrix classes and methods

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 [e-mail]

See Also

SnpMatrix-class, XSnpMatrix-class

Examples

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snpStats documentation built on Nov. 8, 2020, 10:59 p.m.