checkBMIQ: Plot the beta distribution of Infinium I and II probes before...

In LionelRohner/LRTools: A collection of functions written for analyzing Illumina HM450 and EPIC data

Description

This function can be used to evaluate the beta-value distribution of Infinium I and II probes before and after probe bias correction with BMIQ. Although implemented to check BMIQ performance, this function can be used to evaluate Infinium I and II probe distribution at any step of the pipeline and is also not limited to BMIQ-corrected beta-value matrices. By default, the function represents the mean density of Infinium I and II probes across all samples. It may be advisable to check for updates to ChAMP and ChAMPdata as new EPIC manifests are released from time to time.

Usage

checkBMIQ(betaBefore, betaAfter, array = "450K", sampleChoice = NULL)

Arguments

betaBefore	The beta-value matrix before BMIQ correction. The rows should be CpG probes and the columns samples.
betaAfter	The beta-value matrix after BMIQ correction. The rows should be CpG probes and the columns samples.
array	Selection of the array type. For EPIC data use "EPIC" and everything else will be interpreted as HM450 data. By default HM450 data is assumed.
sampleChoice	To check individual samples, enter a sample name as it appears in the column names. Multiple samples can be entered with regular expressions, e.g. ""aPxxx|aPyy"".

Value

No return. A plot should appear in the Plots pane.

Examples

## Not run: checkBMIQ(betaBefore = beta,
                    betaAfter = beta_BMIQcorrected,
                    array = "450K")
## End(Not run)

LionelRohner/LRTools documentation built on Dec. 17, 2021, 1:10 a.m.