update examples (5e66915e) · Commits · github_fork / Presto 20250701

R/pseudobulk.R

+12 −17

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		@@ -25,30 +25,28 @@ compute_hash <- function(data_df, vars_use) {
		return(hash)
		}

		#' Collapse counts
		#' Collapse counts based on multiple categorical metadata columns
		#'
		#' @param counts_mat counts matrix where columns represent cells and rows
		#' represent features
		#' @param meta_data data.frame containing cell metadata
		#' @param varnames subset of `meta_data` column names
		#' @param min_cells_per_group minimum cells to keep collapsed group
		#' @param keep_n keep or drop the `N`` column containing the number of
		#' @param keep_n keep or drop the `N` column containing the number of
		#' cells in each group. Default is `FALSE`
		#' @param how method of collapsing counts from groups. `sum` or `mean`
		#'
		#' @importFrom data.table data.table
		#'
		#' @examples
		#' library(Seurat)
		#' m <- matrix(sample.int(8, 100*500, replace=TRUE),nrow=100, ncol=500)
		#' rownames(m) <- paste0("G", 1:100)
		#' colnames(m) <- paste0("C", 1:500)
		#' o <- CreateSeuratObject(m)
		#' o$md1 <- sample(c("a", "b"), 500, replace=TRUE)
		#' o$md2 <- sample(c("c", "d"), 500, replace=TRUE)
		#' data_collapsed <- collapse_counts(
		#' o@assays$RNA@counts, o@meta.data, c('md1', 'md2')
		#' )
		#' md1 <- sample(c("a", "b"), 500, replace=TRUE)
		#' md2 <- sample(c("c", "d"), 500, replace=TRUE)
		#' df <- data.frame(md1, md2)
		#' data_collapsed <- collapse_counts(m, df, c("md1", "md2"))
		#' head(data_collapsed$$counts_mat)
		#'
		#' @export
		#'
		@@ -364,16 +362,13 @@ pseudobulk_within <- function(
		#'
		#' @examples
		#' \dontrun{
		#' library(Seurat)
		#' m <- matrix(sample.int(8, 100*500, replace=TRUE),nrow=100, ncol=500)
		#' rownames(m) <- paste0("G", 1:100)
		#' colnames(m) <- paste0("C", 1:500)
		#' o <- CreateSeuratObject(m)
		#' o$md1 <- sample(c("a", "b"), 500, replace = TRUE)
		#' o$md2 <- sample(c("c", "d"), 500, replace = TRUE)
		#' data_collapsed <- collapse_counts(
		#' o@assays$RNA@counts, o@meta.data, c('md1', 'md2')
		#' )
		#' md1 <- sample(c("a", "b"), 500, replace=TRUE)
		#' md2 <- sample(c("c", "d"), 500, replace=TRUE)
		#' df <- data.frame(md1, md2)
		#' data_collapsed <- collapse_counts(m, df, c("md1", "md2"))
		#' res_mat <- pseudobulk_deseq2(
		#' ~md1 + md1,
		#' data_collapsed$meta_data,

man/collapse_counts.Rd

+8 −10

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		@@ -2,7 +2,7 @@
		% Please edit documentation in R/pseudobulk.R
		\name{collapse_counts}
		\alias{collapse_counts}
		\title{Collapse counts}
		\title{Collapse counts based on multiple categorical metadata columns}
		\usage{
		collapse_counts(
		counts_mat,
		@@ -23,24 +23,22 @@ represent features}

		\item{min_cells_per_group}{minimum cells to keep collapsed group}

		\item{keep_n}{keep or drop the `N`` column containing the number of
		\item{keep_n}{keep or drop the `N` column containing the number of
		cells in each group. Default is `FALSE`}

		\item{how}{method of collapsing counts from groups. `sum` or `mean`}
		}
		\description{
		Collapse counts
		Collapse counts based on multiple categorical metadata columns
		}
		\examples{
		library(Seurat)
		m <- matrix(sample.int(8, 100*500, replace=TRUE),nrow=100, ncol=500)
		rownames(m) <- paste0("G", 1:100)
		colnames(m) <- paste0("C", 1:500)
		o <- CreateSeuratObject(m)
		o$md1 <- sample(c("a", "b"), 500, replace=TRUE)
		o$md2 <- sample(c("c", "d"), 500, replace=TRUE)
		data_collapsed <- collapse_counts(
		o@assays$RNA@counts, o@meta.data, c('md1', 'md2')
		)
		md1 <- sample(c("a", "b"), 500, replace=TRUE)
		md2 <- sample(c("c", "d"), 500, replace=TRUE)
		df <- data.frame(md1, md2)
		data_collapsed <- collapse_counts(m, df, c("md1", "md2"))
		head(data_collapsed$$counts_mat)

		}

man/pseudobulk_deseq2.Rd

+5 −8

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		@@ -43,16 +43,13 @@ Pseudobulk DESeq2
		}
		\examples{
		\dontrun{
		library(Seurat)
		m <- matrix(sample.int(8, 100*500, replace=TRUE),nrow=100, ncol=500)
		rownames(m) <- paste0("G", 1:100)
		colnames(m) <- paste0("C", 1:500)
		o <- CreateSeuratObject(m)
		o$md1 <- sample(c("a", "b"), 500, replace = TRUE)
		o$md2 <- sample(c("c", "d"), 500, replace = TRUE)
		data_collapsed <- collapse_counts(
		o@assays$RNA@counts, o@meta.data, c('md1', 'md2')
		)
		md1 <- sample(c("a", "b"), 500, replace=TRUE)
		md2 <- sample(c("c", "d"), 500, replace=TRUE)
		df <- data.frame(md1, md2)
		data_collapsed <- collapse_counts(m, df, c("md1", "md2"))
		res_mat <- pseudobulk_deseq2(
		~md1 + md1,
		data_collapsed$meta_data,

vignettes/getting-started.Rmd

+2 −0

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		@@ -77,6 +77,8 @@ group labels.

		```{r}
		data(object_seurat)
		# ensure object structure matches with the installed Seurat version
		object_seurat <- UpdateSeuratObject(object_seurat)
		head(wilcoxauc(object_seurat, 'cell_type'))

		```

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