prepSesame: Apply a chain of sesame preprocessing functions in an...

In zwdzwd/sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

Apply a chain of sesame preprocessing functions in an arbitrary order

Description

Notes on the order of operation: 1. qualityMask and inferSpecies should go before noob and pOOBAH, otherwise the background is too high because of Multi, uk and other probes 2. dyeBias correction needs to happen early 3. channel inference before dyebias 4. noob should happen last, pOOBAH before noob because noob modifies oob

Usage

prepSesame(sdf, prep = "QCDPB", prep_args = NULL)

Arguments

sdf	SigDF
prep	code that indicates preprocessing functions and their execution order (functions on the left is executed first).
prep_args	optional argument list to individual functions, e.g., prepSesame(sdf, prep_args=list(Q=list(mask_names = "design_issue"))) sets qualityMask(sdf, mask_names = "design_issue")

Value

SigDF

Examples

sdf <- sesameDataGet("MM285.1.SigDF")
sdf1 <- prepSesame(sdf, "QCDPB")

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