get_mean_ratio2: Get Mean Ratio for Each Gene x Cell Type

In lahuuki/DeconvoBuddies: Helper Functions for LIBD Deconvolution

Get Mean Ratio for Each Gene x Cell Type

Description

Calculate the mean ratio value and rank for each gene for each cell type in the sce object, to identify effective marker genes for deconvolution.

Usage

get_mean_ratio2(
  sce,
  cellType_col = "cellType",
  assay_name = "logcounts",
  add_symbol = TRUE
)

Arguments

sce	SummarizedExperiment-class object
cellType_col	A character(1) name of the column in the colData() of sce that denotes the cell type or group of interest
assay_name	A character(1) specifying the name of the assay() in the sce object to use to rank expression values. Defaults to logcounts since it typically contains the normalized expression values.
add_symbol	a logical indicating whether the gene symbol column to the marker stats table

Details

Improved efficiency and ability to handle large data sets from get_mean_ratio().

Value

Table of mean ratio for each x cell type

Examples

get_mean_ratio2(sce.test)

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