MSigDBSet-class: MSigDB data set class The Class "MSigDBSet" is used to store...

In wolfsonliu/enrich: Gene list enrichment on KEGG pathway, GO term, Transcript Factor Targets and so on.

Usage

## S4 method for signature 'MSigDBSet'
initialize(.Object, value.vector = NULL,
  STANDARD_NAME = "", SYSTEMATIC_NAME = "", HISTORICAL_NAMES = "",
  ORGANISM = "", PMID = "", AUTHORS = "", GEOID = "",
  EXACT_SOURCE = "", GENESET_LISTING_URL = "", EXTERNAL_DETAILS_URL = "",
  CHIP = "", CATEGORY_CODE = "", SUB_CATEGORY_CODE = "",
  CONTRIBUTOR = "", CONTRIBUTOR_ORG = "", DESCRIPTION_BRIEF = "",
  DESCRIPTION_FULL = "", TAGS = "", MEMBERS = "",
  MEMBERS_SYMBOLIZED = "", MEMBERS_EZID = "", MEMBERS_MAPPING = "",
  FOUNDER_NAMES = "", REFINEMENT_DATASETS = "", VALIDATION_DATASETS = "",
  ...)

## S4 method for signature 'MSigDBSet'
getMembers(.Object, type = c("member", "symbol",
  "entrez"), ...)

Methods (by generic)

• initialize: initialize the MSigDBSet object.

• getMembers: return slot values of MSigDBSet object.

Slots

STANDARD_NAME

character, standard name of the set recently.

SYSTEMATIC_NAME

character, systematic name of the sets, unique and rarely changed.

HISTORICAL_NAMES

character, names of the set used in the past.

ORGANISM

character, organism of the set.

PMID

character, PMID of the set.

AUTHORS

character.

GEOID

character.

EXACT_SOURCE

character.

GENESET_LISTING_URL

character, url of the set in MSigDB.

EXTERNAL_DETAILS_URL

character, url of the set in MSigDB.

CHIP

character.

CATEGORY_CODE

character, category code of set. H: hallmark gene sets. C1: positional gene sets. C2: curated gene sets, with subcategories (CGP, CP, CP:BIOCARTA, CP:KEGG, CP:REACTOME). C3: motif gene sets, with subcategories (MIR, TFT). C4: computational gene sets, with subcategories (CGN, CM). C5: GO gene sets, with subcategories (BP, CC, MF). C6: oncogenic signatures. C7: immunologic signatures.

SUB_CATEGORY_CODE

character, sub category code of set. C2: CGP (chemical and genetic perturbations), CP (Canonical pathways), CP:BIOCARTA (BioCarta gene sets), CP:KEGG (KEGG gene sets), CP:REACTOME (Reactome gene sets). C3: MIR (microRNA targets), TFT (transcription factor targets). C4: CGN (cancer gene neighborhoods), CM (cancer modules). C5: BP (GO biological process), CC (GO cellular component).

CONTRIBUTOR

character.

CONTRIBUTOR_ORG

character.

DESCRIPTION_BRIEF

character, brif description of the set.

DESCRIPTION_FULL

character, detailed description of the set.

TAGS

character.

MEMBERS

character, gene members with label of MSigDB.

MEMBERS_SYMBOLIZED

character, gene members with gene symbol.

MEMBERS_EZID

character, gene members with entrez id.

MEMBERS_MAPPING

character, gene members with mapping of three labels.

FOUNDER_NAMES

character.

REFINEMENT_DATASETS

character.

VALIDATION_DATASETS

character.

Examples

data("msigdb")

genes <- getMembers(
    MSigDB[[1]],
    type = "symbol"
)

genes 

wolfsonliu/enrich documentation built on May 4, 2019, 9:47 a.m.