findMarkers_1vAll: Calculate 1 vs. All standard fold change for each gene x cell...

In lahuuki/DeconvoBuddies: Helper Functions for LIBD Deconvolution

Calculate 1 vs. All standard fold change for each gene x cell type, wrapper function for scran::findMarkers

Description

Calculate 1 vs. All standard fold change for each gene x cell type, wrapper function for scran::findMarkers

Usage

findMarkers_1vAll(
  sce,
  assay_name = "counts",
  cellType_col = "cellType",
  add_symbol = FALSE,
  mod = "~donor",
  verbose = TRUE
)

Arguments

sce	single cell experiment object
assay_name	Name of the assay to use for calculation
cellType_col	Column name on colData of the sce that denotes the celltype
add_symbol	Add the gene symbol column to the marker stats table
mod	String specifying the model used as design in findMarkers. Can be NULL if there are no blocking terms with uninteresting factors as documented at pairwiseTTests.
verbose	Boolean choosing to print progress messages or not

Value

Table of 1 vs. ALL std log fold change + p-values for each gene x cell type

Examples

markers_1vAll <- findMarkers_1vAll(sce_ab)
head(markers_1vAll)

lahuuki/DeconvoBuddies documentation built on May 5, 2024, 9:35 a.m.