flags {oligoClasses} | R Documentation

## Batch-level summary of SNP flags.

### 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))

[Package oligoClasses version 1.56.0 Index]