qualityMask: Mask beta values by design quality
In zwdzwd/sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

qualityMask

R Documentation

Mask beta values by design quality

Description

Currently quality masking only supports three platforms see also listAvailableMasks(sdfPlatform(sdf))

Usage

qualityMask(sdf, mask_names = "recommended", verbose = TRUE)

Arguments

`sdf`	a `SigDF` object
`mask_names`	a vector of masking groups, see listAvailableMasks use "recommended" for recommended masking. One can also combine "recommended" with other masking groups by specifying a vector, e.g., c("recommended", "M_mapping")
`verbose`	be verbose

Value

a filtered SigDF

Examples

sesameDataCache() # if not done yet
sdf <- sesameDataGet('EPIC.1.SigDF')
sum(sdf$mask)
sum(qualityMask(sdf)$mask)
sum(qualityMask(sdf, mask_names = NULL)$mask)

## list available masks, the dbname column
listAvailableMasks(sdfPlatform(sdf))
listAvailableMasks("EPICv2")

zwdzwd/sesame documentation built on Dec. 21, 2024, 1:20 p.m.