getAlleleProbePairs.AffymetrixCdfFile: Gets the indices of probepairs with the same pair of SNP...

In HenrikBengtsson/aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

Gets the indices of probepairs with the same pair of SNP nucleotides

Description

Gets the indices of probepairs with the same pair of SNP nucleotides. Note that the order of allele A and allele B is irrelevant. For instance, all probepairs with nucleotides (A,T) are calibrated together with all probepairs with nucleotides (T,A) reversed.

Usage

## S3 method for class 'AffymetrixCdfFile'
getAlleleProbePairs(this, units=NULL, ignoreOrder=TRUE, force=FALSE, verbose=FALSE, ...)

Arguments

verbose	A logical or a Verbose object.
...	Not used.

Value

Returns a named list where each element is a two-column matrix where the column names are the nucleotides for the two alleles.

Benchmarking

On an IBM Thinkpad A31 with 1.8GHz and 1GB RAM:

Mapping10K_Xba142

10208 units & 432964 cells: 11 seconds.

Mapping50K_Xba240

58960 SNPs & 589,600 (PMA,PMB) probe pairs: 11 seconds.

Author(s)

Henrik Bengtsson

See Also

For more information see AffymetrixCdfFile.

HenrikBengtsson/aroma.affymetrix documentation built on Feb. 20, 2024, 9:07 p.m.