KYCG_buildGeneDBs: build gene-probe association database

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

build gene-probe association database

Description

build gene-probe association database

Usage

KYCG_buildGeneDBs(
  query = NULL,
  platform = NULL,
  genome = NULL,
  max_distance = 10000,
  silent = FALSE
)

Arguments

query	the query probe list. If NULL, use all the probes on the platform
platform	HM450, EPIC, MM285, Mammal40, will infer from query if not given
genome	hg38, mm10, ..., will infer if not given. For additional mapping, download the GRanges object from http://zwdzwd.github.io/InfiniumAnnotation and provide the following argument ..., genome = sesameAnno_buildManifestGRanges("downloaded_file"),... to this function.
max_distance	probe-gene distance for association
silent	suppress messages

Value

gene databases

Examples

query <- c("cg04707299", "cg13380562", "cg00480749")
dbs <- KYCG_buildGeneDBs(query, platform = "EPIC")
testEnrichment(query, dbs, platform = "EPIC")

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