minfiQC: easy one-step QC of methylation object

In hansenlab/minfi: Analyze Illumina Infinium DNA methylation arrays

easy one-step QC of methylation object

Description

This function combines a number of functions into a simple to use, one step QC step/

Usage

minfiQC(object, fixOutliers = TRUE, verbose = FALSE)

Arguments

object	An object of class [Genomic]MethylSet.
fixOutliers	Should the function fix outlying observations (using fixMethOutliers) before running QC?
verbose	Should the function be verbose?

Details

A number of functions are run sequentially on the object.

First outlier values are thresholded using fixMethOutliers. Then qc is performed using getQC and then sample specific sex is estimated using getSex.

Value

A list with two values,

object	The object processed by fixMethOutliers and with a column predictedSex added to the pheno data.
qc	A DataFrame with columns from the output of getQC and getSex

Author(s)

Kasper D. Hansen

See Also

getSex, getQC, fixMethOutliers

Examples

if(require(minfiData)) {
  out <- minfiQC(MsetEx)
  ## plotQC(out$qc)
  ## plotSex(out$sex)
}

hansenlab/minfi documentation built on Feb. 2, 2024, 11:23 a.m.