get_probes: Update probes of interest.

In markgene/yamatClassifier: Yet Another Methylation Array Toolkit: Classifier

Update probes of interest.

Description

If probe set is not set for YamatClassifierTrainer, check if a Rda file exists for probe set. If exists, load Rda file. Otherwise, get probe IDs from scratch. The probe set has:

• Drop SNP.

• Drop loci on chr X or Y..

• Common between the array types of trainer and EPIC v2

Usage

get_probes(trainer, chip_type_name = NULL, present_by_epic_v2 = TRUE)

Arguments

trainer	A S3 object of YamatClassifierTrainer class.
chip_type_name	column contains the chip type name.
present_by_epic_v2	bool if only include probes present in EPIC v2.

Details

If probe set is set, returns it and meanwhile save it in Rda file if the file does not exist.

Value

a list of probe CG IDs.

markgene/yamatClassifier documentation built on Oct. 14, 2024, 2:36 a.m.