switch.alleles: Switch alleles in columns of a SnpMatrix or in test results

In snpStats: SnpMatrix and XSnpMatrix classes and methods

Description

This is a generic function which can be applied to objects of class "SnpMatrix" or "XSnpMatrix" (which hold SNP genotype data), or to objects of class "SingleSnpTestsScore" or "GlmTests" (which hold association test results). In the former case, specified SNPs can be recoded as if the alleles were switched (so that AA genotypes become BB and vice-versa while AB remain unchanged). In the latter case, test results are modified as if alleles had been switched.

Usage

switch.alleles(x, snps)

Arguments

x	The input object, of class "SnpMatrix", "XSnpMatrix", "SingleSnpTestsScore", or "GlmTests"
snps	A vector of type integer, character or logical specifying the SNP to have its alleles switched

Value

An object of the same class as the input object

Note

Switching alleles for SNPs has no effect on test results. These functions are required when carrying out meta-analysis, bringing together several sets of results. It is then important that alleles line up in the datasets to be combined. It is often more convenient (and faster) to apply this process to the test result objects rather than to the genotype data themselves.

Author(s)

David Clayton [e-mail]

See Also

SnpMatrix-class, XSnpMatrix-class, SingleSnpTests-class, GlmTests-class

Examples

data(testdata)
which <-  c("173774", "173811")
Asw <- switch.alleles(Autosomes, which)
col.summary(Autosomes[,which])
col.summary(Asw[,which])

Example output

Loading required package: survival
Loading required package: Matrix
       Calls Call.rate Certain.calls       RAF       MAF       P.AA      P.AB
173774   388 0.9797980             1 0.8569588 0.1430412 0.03092784 0.2242268
173811   343 0.8661616             1 0.1545190 0.1545190 0.71428571 0.2623907
             P.BB      z.HWE
173774 0.74484536 -1.6819712
173811 0.02332362  0.0783225
Warning message:
In col.summary(Autosomes[, which]) :
  4 rows were empty - ignored when calculating call rates
       Calls Call.rate Certain.calls       RAF       MAF       P.AA      P.AB
173774   388 0.9797980             1 0.1430412 0.1430412 0.74484536 0.2242268
173811   343 0.8661616             1 0.8454810 0.1545190 0.02332362 0.2623907
             P.BB      z.HWE
173774 0.03092784 -1.6819712
173811 0.71428571  0.0783225
Warning message:
In col.summary(Asw[, which]) :
  4 rows were empty - ignored when calculating call rates

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