genotypeAffy: Genotype Affymetrix CEL files
In crlmm: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays

Description Usage Arguments Details Value Author(s) See Also

View source: R/cnrma-functions.R

Assign diallelic genotypes at polymorphic markers

1	genotypeAffy(cnSet, SNRMin = 5, recallMin = 10, recallRegMin = 1000, gender = NULL, badSNP = 0.7, returnParams = TRUE, verbose = TRUE)

`cnSet`	An object of class `CNSet`
`SNRMin`	See `crlmm`
`recallMin`	See `crlmm`
`recallRegMin`	See `crlmm`
`gender`	See `crlmm`
`badSNP`	See `crlmm`
`returnParams`	See `crlmm`
`verbose`	Logical.

Wrapper for crlmm genotyping.

Returns logical. SNP genotypes and confidence scores are written to ff_matrix objects.

R.Scharpf

crlmm, calls, confs

crlmm documentation built on Nov. 8, 2020, 4:55 p.m.

crlmm index

Package overview Copy number estimation crlmm Vignette - Downstream Analysis crlmm Vignette - Genotyping crlmm Vignette - Illumina 370k chip From Genotypes to Association IlluminaPreprocessCN Vignette for Illumina Infrastructure for copy number analysis Infrastructure for copy number analysis Overview of copy number vignettes Preprocessing and genotyping Illumina arrays for copy number analysis

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