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Move all generic functions to a separate file "AllGenerics.R". Also add a cross-platform check of devel R.

Gene233 authored on 11/04/2023 07:27:48
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man/get_gsc_sig.Rd
History View file @ 984c56d
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@@ -1,5 +1,5 @@
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 % Generated by roxygen2: do not edit by hand
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-% Please edit documentation in R/get_gsc_sig.R
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+% Please edit documentation in R/AllGenerics.R, R/get_gsc_sig-methods.R
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 \name{get_gsc_sig}
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 \alias{get_gsc_sig}
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 \alias{get_gsc_sig,GeneSetCollection,character-method}
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Change names of imported data from upper case to lower case.

Gene233 authored on 23/03/2023 04:04:19
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man/get_gsc_sig.Rd
History View file @ 0779768
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@@ -74,6 +74,7 @@ By setting cat and subcat, matching can be constrained in the union of given
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 categories and subcategories if gsc = 'msigdb'.
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 }
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 \examples{
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+data("msigdb_gobp_nk")
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 get_gsc_sig(
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   gsc = msigdb_gobp_nk,
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   pattern = "natural_killer_cell_mediated",
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Fix spelling mistakes.

Gene233 authored on 22/03/2023 10:45:36
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man/get_gsc_sig.Rd
History View file @ 701e6ea
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@@ -57,7 +57,7 @@ The sub-category(s) must be one from
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 \item{species}{character, species of interest, can be 'hs' or 'mm'}
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 \item{id}{a character, representing the ID type to use ("SYM" for gene
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-symbols and "EZID" for Entrez IDs)}
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+SYMBOLs and "EZID" for ENTREZ IDs)}
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 \item{version}{a character, stating the version of MSigDB to be retrieved
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 (should be >= 7.2). See \code{\link[msigdb:getMsigdbVersions]{msigdb::getMsigdbVersions()}}.}
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@@ -68,7 +68,7 @@ symbols and "EZID" for Entrez IDs)}
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 A GeneSet object containing all matched gene-sets in MSigDB
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 }
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 \description{
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-Collect genesets from MSigDB or given GeneSetCollection, of which the gene-set
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+Collect gene sets from MSigDB or given GeneSetCollection, of which the gene-set
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 names are matched to the given regex pattern by using \code{\link[=grep]{grep()}} function.
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 By setting cat and subcat, matching can be constrained in the union of given
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 categories and subcategories if gsc = 'msigdb'.
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Update markers pool generation functions and deg functions.

Gene233 authored on 28/02/2023 01:18:59
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man/get_gsc_sig.Rd
History View file @ b4b0fa5
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new file mode 100644
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@@ -0,0 +1,83 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/get_gsc_sig.R
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+\name{get_gsc_sig}
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+\alias{get_gsc_sig}
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+\alias{get_gsc_sig,GeneSetCollection,character-method}
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+\alias{get_gsc_sig,character,character-method}
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+\title{Collect genes from MSigDB or provided GeneSetCollection.}
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+\usage{
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+get_gsc_sig(
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+  gsc = "msigdb",
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+  pattern,
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+  cat = NULL,
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+  subcat = NULL,
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+  species = c("hs", "mm"),
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+  id = c("SYM", "EZID"),
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+  version = msigdb::getMsigdbVersions(),
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+  ...
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+)
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+
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+\S4method{get_gsc_sig}{GeneSetCollection,character}(
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+  gsc = "msigdb",
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+  pattern,
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+  cat = NULL,
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+  subcat = NULL,
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+  species = c("hs", "mm"),
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+  id = c("SYM", "EZID"),
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+  version = msigdb::getMsigdbVersions(),
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+  ...
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+)
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+
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+\S4method{get_gsc_sig}{character,character}(
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+  gsc = "msigdb",
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+  pattern,
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+  cat = NULL,
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+  subcat = NULL,
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+  species = c("hs", "mm"),
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+  id = c("SYM", "EZID"),
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+  version = msigdb::getMsigdbVersions(),
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+  ...
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+)
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+}
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+\arguments{
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+\item{gsc}{'msigdb' or GeneSetCollection to be searched}
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+
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+\item{pattern}{pattern pass to \code{\link[=grep]{grep()}}, to match the MsigDB gene-set name of
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+interest, e.g. 'NATURAL_KILLER_CELL_MEDIATED'}
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+
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+\item{cat}{character, stating the category(s) to be retrieved.
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+The category(s) must be one from \code{\link[msigdb:listCollections]{msigdb::listCollections()}},
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+see details in \code{\link[msigdb:subsetCollection]{msigdb::subsetCollection()}}}
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+
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+\item{subcat}{character, stating the sub-category(s) to be retrieved.
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+The sub-category(s) must be one from
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+\code{\link[msigdb:listSubCollections]{msigdb::listSubCollections()}}, see details in
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+\code{\link[msigdb:subsetCollection]{msigdb::subsetCollection()}}}
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+
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+\item{species}{character, species of interest, can be 'hs' or 'mm'}
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+
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+\item{id}{a character, representing the ID type to use ("SYM" for gene
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+symbols and "EZID" for Entrez IDs)}
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+
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+\item{version}{a character, stating the version of MSigDB to be retrieved
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+(should be >= 7.2). See \code{\link[msigdb:getMsigdbVersions]{msigdb::getMsigdbVersions()}}.}
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+
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+\item{...}{params for \code{\link[=grep]{grep()}}, used to match pattern to gene-set names}
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+}
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+\value{
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+A GeneSet object containing all matched gene-sets in MSigDB
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+}
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+\description{
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+Collect genesets from MSigDB or given GeneSetCollection, of which the gene-set
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+names are matched to the given regex pattern by using \code{\link[=grep]{grep()}} function.
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+By setting cat and subcat, matching can be constrained in the union of given
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+categories and subcategories if gsc = 'msigdb'.
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+}
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+\examples{
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+get_gsc_sig(
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+  gsc = msigdb_gobp_nk,
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+  pattern = "natural_killer_cell_mediated",
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+  subcat = "GO:BP",
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+  ignore.case = TRUE
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+)
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+}