KYCG_annoProbes: Annotate Probe IDs using KYCG databases

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

Annotate Probe IDs using KYCG databases

Description

see sesameData_annoProbes if you'd like to annotate by genomic coordinates (in GRanges)

Usage

KYCG_annoProbes(
  query,
  databases,
  db_names = NULL,
  platform = NULL,
  sep = ",",
  indicator = FALSE,
  silent = FALSE
)

Arguments

query	probe IDs in a character vector
databases	character or actual database (i.e. list of probe IDs)
db_names	specific database (default to all databases)
platform	EPIC, MM285 etc. will infer from probe IDs if not given
sep	delimiter used in paste
indicator	return the indicator matrix instead of a concatenated annotation (in the case of have multiple annotations)
silent	suppress message

Value

named annotation vector, or indicator matrix

Examples

query <- names(sesameData_getManifestGRanges("MM285"))
anno <- KYCG_annoProbes(query, "designGroup", silent = TRUE)

zwdzwd/sesame documentation built on April 28, 2024, 12:48 p.m.