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andrewdchenandrewdchen
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msigdb updates
1 parent 410930d commit 5fbf99e

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Lines changed: 84 additions & 65 deletions

‎DESCRIPTION‎

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@@ -12,7 +12,7 @@ Depends: R (>= 3.6.0)
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License: GPL-3 + file LICENSE
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URL: https://github.com/montilab/hypeR
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Encoding: UTF-8
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RoxygenNote: 7.2.3
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RoxygenNote: 7.3.1
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LazyData: false
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Imports:
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ggplot2,

‎R/db_msig.R‎

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@@ -42,7 +42,7 @@ msigdb_check_species <- function(species="") {
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#' Get msigdbr available genesets
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#'
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#' @param species A species to determine gene symbols (refer to ?msigdbr::msigdbr for avilable species)
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#' @param species A species to determine gene symbols (refer to ?msigdbr::msigdbr for available species)
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#' @return A dataframe of available genesets
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#'
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#' @examples
@@ -60,10 +60,10 @@ msigdb_available <- function(species="Homo sapiens") {
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# Gene set categories
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msigdbr(species=species) %>%
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dplyr::select(gs_cat, gs_subcat) %>%
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dplyr::select(gs_collection, gs_subcollection) %>%
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unique() %>%
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dplyr::arrange(gs_cat, gs_subcat) %>%
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magrittr::set_colnames(c("Category", "Subcategory"))
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dplyr::arrange(gs_collection, gs_subcollection) %>%
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magrittr::set_colnames(c("Collection", "Subcollection"))
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}
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#' Print msigdb gsets information
@@ -96,7 +96,7 @@ msigdb_info <- function() {
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cat("|------------------------------------------------------------------|\n")
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cat("| Available Genesets |\n")
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cat("|------------------------------------------------------------------|\n")
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cat("| Category Subcategory | Description |\n")
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cat("| Collection Subcollection | Description |\n")
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cat("|------------------------------------------------------------------|\n")
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cat("| C1 | Positional |\n")
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cat("| C2 CGP | Chemical and Genetic Perturbations |\n")
@@ -122,30 +122,46 @@ msigdb_info <- function() {
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#' Download data from msigdb in the form of a named list
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#'
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#' @param species A species to determine gene symbols (refer to ?msigdbr::msigdbr for avilable species)
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#' @param category Geneset category (refer to ?msigdbr::msigdbr for avilable categories)
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#' @param subcategory Geneset subcategory (refer to ?msigdbr::msigdbr for avilable subcategories)
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#' @param species A species to determine gene symbols (refer to ?msigdbr::msigdbr for available species)
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#' @param collection Geneset collection (refer to ?msigdbr::msigdbr_collections for available categories)
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#' @param subcollection Geneset subcollection (refer to ?msigdbr::msigdbr_collections for available subcategories)
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#' @return A list of genesets
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#'
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#' @examples
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#' HALLMARK <- msigdb_download("Homo sapiens", "H", "")
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#' HALLMARK_HUMAN <- msigdb_download("Homo sapiens", "H")
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#' HALLMARK_MOUSE <- msigdb_download("Mus musculus", "MH")
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#'
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#' @importFrom magrittr %>%
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#' @importFrom dplyr select
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#' @importFrom msigdbr msigdbr
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#' @export
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msigdb_download <- function(species, category, subcategory="") {
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msigdb_download <- function(species, collection, subcollection=NULL) {
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# Check species
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msigdb_check_species(species)
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response <- msigdbr(species, category, subcategory)
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if(species == "Homo sapiens") {
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db_species = "HS"
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} else if (species == "Mus musculus") {
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db_species = "MM"
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} else {
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# For non-human species msigdb will use gene orthologs from the human database.
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db_species == "HS"
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}
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response <- msigdbr(species = species,
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db_species = db_species,
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collection = collection,
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subcollection = subcollection)
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if (nrow(response) == 0) {
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stop("No data found: Please review available species and genesets\n", msigdb_info())
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}
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# Download genesets
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mdf <- msigdbr(species, category, subcategory) %>%
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mdf <- msigdbr(species = species,
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collection = collection,
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db_species = db_species,
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subcollection = subcollection) %>%
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dplyr::select(gs_name, gene_symbol) %>%
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dplyr::distinct()
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@@ -156,19 +172,20 @@ msigdb_download <- function(species, category, subcategory="") {
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#' Download data from msigdb in the form of a gsets object
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#'
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#' @param species A species to determine gene symbols (refer to ?msigdbr::msigdbr for avilable species)
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#' @param category Geneset category (refer to ?msigdbr::msigdbr for avilable categories)
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#' @param subcategory Geneset subcategory (refer to ?msigdbr::msigdbr for avilable subcategories)
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#' @param species A species to determine gene symbols (refer to ?msigdbr::msigdbr_species for available species)
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#' @param collection Geneset collection (refer to ?msigdbr::msigdbr_collections for available categories)
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#' @param subcollection Geneset subcollection (refer to ?msigdbr::msigdbr_collections for available subcategories)
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#' @param clean Use true to clean labels of genesets
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#' @return A gsets object
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#'
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#' @examples
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#' HALLMARK <- msigdb_gsets("Homo sapiens", "H", "")
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#' HALLMARK_HUMAN <- msigdb_gsets("Homo sapiens", "H")
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#' HALLMARK_MOUSE <- msigdb_gsets("Mus musculus", "MH")
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#'
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#' @export
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msigdb_gsets <- function(species, category, subcategory="", clean=FALSE) {
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genesets <- msigdb_download(species, category, subcategory)
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name <- ifelse(subcategory == "", category, paste(category, subcategory, sep="."))
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msigdb_gsets <- function(species, collection, subcollection=NULL, clean=FALSE) {
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genesets <- msigdb_download(species, collection, subcollection)
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name <- ifelse(is.null(subcollection), collection, paste(collection, subcollection, sep="."))
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version <- msigdb_version()
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gsets$new(genesets, name=name, version=version, clean=clean)
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}

‎R/hyp_dots.R‎

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@@ -235,7 +235,7 @@
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#' @return A ggplot object
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#'
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#' @examples
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#' genesets <- msigdb_gsets("Homo sapiens", "C2", "CP:KEGG")
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#' genesets <- msigdb_gsets("Homo sapiens", "C2", "CP:KEGG_LEGACY")
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#'
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#' signature <- c("IDH3B","DLST","PCK2","CS","PDHB","PCK1","PDHA1","LOC642502",
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#' "PDHA2","LOC283398","FH","SDHD","OGDH","SDHB","IDH3A","SDHC",

‎R/hyp_emap.R‎

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@@ -107,7 +107,7 @@
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#' @return A visNetwork object
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#'
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#' @examples
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#' genesets <- msigdb_gsets("Homo sapiens", "C2", "CP:KEGG")
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#' genesets <- msigdb_gsets("Homo sapiens", "C2", "CP:KEGG_LEGACY")
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#'
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#' signature <- c("IDH3B","DLST","PCK2","CS","PDHB","PCK1","PDHA1","LOC642502",
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#' "PDHA2","LOC283398","FH","SDHD","OGDH","SDHB","IDH3A","SDHC",

‎R/hyp_show.R‎

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@@ -5,7 +5,7 @@
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#' @return A reactable table
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#'
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#' @examples
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#' genesets <- msigdb_gsets("Homo sapiens", "C2", "CP:KEGG")
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#' genesets <- msigdb_gsets("Homo sapiens", "C2", "CP:KEGG_LEGACY")
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#'
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#' signature <- c("IDH3B","DLST","PCK2","CS","PDHB","PCK1","PDHA1","LOC642502",
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#' "PDHA2","LOC283398","FH","SDHD","OGDH","SDHB","IDH3A","SDHC",

‎R/hyp_to_excel.R‎

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@@ -7,7 +7,7 @@
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#' @return NULL
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#'
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#' @examples
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#' genesets <- msigdb_gsets("Homo sapiens", "C2", "CP:KEGG")
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#' genesets <- msigdb_gsets("Homo sapiens", "C2", "CP:KEGG_LEGACY")
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#'
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#' signature <- c("IDH3B","DLST","PCK2","CS","PDHB","PCK1","PDHA1","LOC642502",
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#' "PDHA2","LOC283398","FH","SDHD","OGDH","SDHB","IDH3A","SDHC",

‎R/hyp_to_table.R‎

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@@ -8,7 +8,7 @@
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#' @return NULL
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#'
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#' @examples
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#' genesets <- msigdb_gsets("Homo sapiens", "C2", "CP:KEGG")
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#' genesets <- msigdb_gsets("Homo sapiens", "C2", "CP:KEGG_LEGACY")
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#'
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#' signature <- c("IDH3B","DLST","PCK2","CS","PDHB","PCK1","PDHA1","LOC642502",
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#' "PDHA2","LOC283398","FH","SDHD","OGDH","SDHB","IDH3A","SDHC",

‎R/hype.R‎

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@@ -13,7 +13,7 @@
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#' @return A hyp object
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#'
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#' @examples
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#' genesets <- msigdb_gsets("Homo sapiens", "C2", "CP:KEGG")
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#' genesets <- msigdb_gsets("Homo sapiens", "C2", "CP:KEGG_LEGACY")
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#'
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#' signature <- c("IDH3B","DLST","PCK2","CS","PDHB","PCK1","PDHA1","LOC642502",
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#' "PDHA2","LOC283398","FH","SDHD","OGDH","SDHB","IDH3A","SDHC",

‎R/reactable.R‎

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@@ -8,7 +8,7 @@
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#' @param hyp_hmap_args A list of keyword arguments passed to hyp_hmap
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#'
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#' @examples
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#' genesets <- msigdb_gsets("Homo sapiens", "C2", "CP:KEGG")$genesets[1:5]
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#' genesets <- msigdb_gsets("Homo sapiens", "C2", "CP:KEGG_LEGACY")$genesets[1:5]
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#'
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#' signature <- c("IDH3B","DLST","PCK2","CS","PDHB","PCK1","PDHA1","LOC642502",
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#' "PDHA2","LOC283398","FH","SDHD","OGDH","SDHB","IDH3A","SDHC",
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#' @param hyp_hmap_args A list of keyword arguments passed to hyp_hmap
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#'
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#' @examples
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#' genesets <- msigdb_gsets("Homo sapiens", "C2", "CP:KEGG")$genesets[1:5]
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#' genesets <- msigdb_gsets("Homo sapiens", "C2", "CP:KEGG_LEGACY")$genesets[1:5]
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#'
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#' experiment <- list("S1"=c("IDH3B","DLST","PCK2","CS","PDHB","PCK1","PDHA1","LOC642502"),
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#' "S2"=c("PDHA2","LOC283398","FH","SDHD","OGDH","SDHB","IDH3A","SDHC"))
@@ -132,7 +132,7 @@ rctbl_mhyp <- function(mhyp,
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#' @param ... Arguments passed to table generators
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#'
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#' @examples
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#' genesets <- msigdb_gsets("Homo sapiens", "C2", "CP:KEGG")$genesets[1:5]
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#' genesets <- msigdb_gsets("Homo sapiens", "C2", "CP:KEGG_LEGACY")$genesets[1:5]
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#'
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#' experiment <- list("S1"=c("IDH3B","DLST","PCK2","CS","PDHB","PCK1","PDHA1","LOC642502"),
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#' "S2"=c("PDHA2","LOC283398","FH","SDHD","OGDH","SDHB","IDH3A","SDHC"))

‎R/utils.R‎

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@@ -3,7 +3,7 @@
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#' @param x A vector of labels
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#'
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#' @examples
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#' HALLMARK <- msigdb_download("Homo sapiens", "H", "")
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#' HALLMARK <- msigdb_download("Homo sapiens", "H")
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#' names(HALLMARK) <- clean_genesets(names(HALLMARK))
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#' head(names(HALLMARK))
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#'

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