enrichR waits 5 seconds (28a1da79) · Commits · github_fork / HdWGCNA

DESCRIPTION

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		Package: hdWGCNA
		Title: hdWGCNA
		Version: 0.2.17
		Version: 0.2.18
		Authors@R: c(
		person("Sam", "Morabito", , "smorabit@uci.edu", role = c("aut", "cre"),
		comment = c(ORCID = "0000-0002-7768-4856")),

NEWS.md

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		# hdWGCNA 0.2.18 (2023-04-14)
		## Added
		- None.

		## Changes
		- We noticed on rare occasion that EnrichR would give duplicated results for different modules, so we added a new option in `RunEnrichr` to wait in between sending requests to the EnrichR server (default is 5 seconds).

		# hdWGCNA 0.2.17 (2023-03-27)
		## Added
		- None.

R/Enrichment.R

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		@@ -6,21 +6,32 @@
		#' @param seurat_obj A Seurat object
		#' @param dbs character vector of EnrichR databases
		#' @param max_genes Max number of genes to include per module, ranked by kME.
		#' @param wait logical indicating whether or not to wait some time between sending requests to the EnrichR server.
		#' @param wait_time the number of seconds to wait between sending requests to the EnrichR server. Value must be less than 60.
		#' @param wgcna_name The name of the hdWGCNA experiment in the seurat_obj@misc slot
		#' @keywords scRNA-seq
		#' @export
		#' @examples
		#' RunEnrichr
		RunEnrichr <- function(
		seurat_obj,
		dbs = c('GO_Biological_Process_2021','GO_Cellular_Component_2021','GO_Molecular_Function_2021'),
		max_genes = 100,
		wait = TRUE,
		wait_time = 5,
		wgcna_name=NULL, ...
		){

		# get data from active assay if wgcna_name is not given
		if(is.null(wgcna_name)){wgcna_name <- seurat_obj@misc$active_wgcna}

		# check wait_time
		if(!is.numeric(wait_time)){
		stop(paste0('wait_time must be a numeric.'))
		}
		if(wait_time > 60 \| wait_time < 1){
		stop(paste0('Invalid value selected for wait_time, must be greater than 0 and less than 60.'))
		}

		# get modules:
		modules <- GetModules(seurat_obj, wgcna_name)
		mods <- levels(modules$module)
		@@ -39,10 +50,13 @@ RunEnrichr <- function(
		} else{
		cur_genes <- subset(modules, module == cur_mod) %>% .$gene_name %>% as.character
		}

		# run the enrichment test
		enriched <- enrichR::enrichr(cur_genes, dbs)

		if(wait){
		Sys.sleep(wait_time)
		}

		# collapse into one db
		for(db in names(enriched)){
		cur_df <- enriched[[db]]
		@@ -72,7 +86,6 @@ RunEnrichr <- function(
		#' @param wgcna_name The name of the hdWGCNA experiment in the seurat_obj@misc slot
		#' @keywords scRNA-seq
		#' @export
		#' @examples
		#' OverlapModulesDEGs
		OverlapModulesDEGs <- function(
		seurat_obj,

docs/404.html

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		@@ -39,7 +39,7 @@
		</button>
		<span class="navbar-brand">
		<a class="navbar-link" href="https://smorabit.github.io/hdWGCNA/index.html">hdWGCNA</a>
		<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.2.17</span>
		<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.2.18</span>
		</span>
		</div>

docs/LICENSE-text.html

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		@@ -17,7 +17,7 @@
		</button>
		<span class="navbar-brand">
		<a class="navbar-link" href="index.html">hdWGCNA</a>
		<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.2.17</span>
		<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.2.18</span>
		</span>
		</div>

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