flags: Batch-level summary of SNP flags.

In jmacdon/oligoClasses: Classes for high-throughput arrays supported by oligo and crlmm

Description

Used to flag SNPs with low minor allele frequencies, or for possible problems during the CN estimation step. Currently, this is primarily more for internal use.

Usage

flags(object)

Arguments

object

An object of class CNSet

Value

A matrix or ff_matrix object with rows corresponding to markers and columns corresponding to batch.

See Also

batchStatistics

Examples

x <- matrix(runif(250*96*2, 0, 2), 250, 96*2)
test1 <- new("CNSet", alleleA=x, alleleB=x, call=x, callProbability=x,
	      batch=as.character(rep(letters[1:2], each=96)))
dim(flags(test1))

jmacdon/oligoClasses documentation built on Aug. 11, 2020, 12:32 a.m.