LoadGeneSets: LoadGeneSets

In TranslationalBioinformaticsUnit/GeneSetCluster: Cluster together Gene-Sets from Gene Set Analysis

LoadGeneSets

Description

Automatic loader for gene sets from the IPA and Great tools.

Usage

LoadGeneSets(file_location = canonical.files,
  groupnames = c("MClust_1", "MClust_26", "MClust_3457"),
  P.cutoff = 1.3, Mol.cutoff = 5, Source = "IPA",
  Great.Background = F, type = "Canonical_Pathways", topranks = "",
  structure = "SYMBOL", Organism = "org.Mm.eg.db", seperator = ",")

Arguments

file_location	A location string in a vector.
groupnames	A vector with group names of the different gene set experiments
P.cutoff	numeric Pvalue cutoff for filtering.
Mol.cutoff	numeric value for minimum number of molecules.
Source	Tool used to generate gene sets.
Great.Background	If the Great tool was used, did the user supply a background.
type	For IPA data if Canonical pathways or Functional Anotations were supplied.
topranks	numeric with the number of ranks per group to be loaded, usefull when there is a lot of data.
structure	The structure of the genes. is it SYMBOLS, ENSEMBL, NCBI etc. Used for converting when there is mutiple structure in the object.
Organism	the package name for the human or mouse data, used for converting the gene structure. name of the package, currently org.Hs.eg.db and org.Mm.eg.db supported.
seperator	A character used within in the string to seperate genes

Value

a pathwayobject

Examples

Great.files <- c(system.file("extdata", "MM10.GREAT.KO.uGvsMac.bed.tsv",
                             package = "GeneSetCluster"),
system.file("extdata", "MM10.GREAT.KO.uGvsMac.bed_BCKGRND.tsv", package = "GeneSetCluster"),
system.file("extdata", "MM10.GREAT.WT.uGvsMac.bed.tsv", package = "GeneSetCluster"),
system.file("extdata", "MM10.GREAT.WT.uGvsMac.bed_BCKGRND.tsv", package = "GeneSetCluster"))
Great.files.bckgrnd <- Great.files[grepl("BCKGRND", Great.files)]


Great.bckgnrd.Object1 <- LoadGeneSets(file_location = Great.files.bckgrnd,
                                      groupnames= c("KO", "WT"),
                                      P.cutoff = 0.05,
                                      Mol.cutoff = 5,
                                      Source = "Great",
                                      Great.Background = TRUE,
                                      type = "Canonical_Pathways",
                                    topranks = 20,
                                   structure = "SYMBOL",
                                   Organism = "org.Mm.eg.db",
                                   seperator = ",")

TranslationalBioinformaticsUnit/GeneSetCluster documentation built on Feb. 2, 2023, 4:06 a.m.