removeLowQualitySamples: Quality control of SnpSetIllumina objects

In beadarraySNP: Normalization and reporting of Illumina SNP bead arrays

Description

Remove samples from a SnpSetIllumina object that show a low quality

Usage

removeLowQualitySamples(object, min.intensity = 1500, min.gt = 100, subsample = "OPA")

Arguments

object	SnpSetIllumina-class object
min.intensity	numeric. Samples that show a median intensity below this value in either Red or Green channel are removed
min.gt	numeric. Samples that have less than this amount of valid genotypes are removed
subsample	factor or column name in featureData slot of object

Value

This function returns an SnpSetIllumina object.

Author(s)

Jan Oosting

Examples

  data(chr17.260)
  chr17.260<-removeLowQualitySamples(chr17.260,min.gt=10)

beadarraySNP documentation built on Nov. 8, 2020, 7:21 p.m.