tof_analyze_expression: Perform Differential Expression Analysis (DEA) on...

In keyes-timothy/tidytof: Analyze High-dimensional Cytometry Data Using Tidy Data Principles

Perform Differential Expression Analysis (DEA) on high-dimensional cytometry data

Description

This function performs differential expression analysis on the cell clusters contained within a 'tof_tbl' using one of three methods ("diffcyt", "glmm", and "ttest"). It wraps the members of the 'tof_analyze_expression_*' function family: tof_analyze_expression_diffcyt, tof_analyze_expression_lmm, and tof_analyze_expression_ttest.

Usage

tof_analyze_expression(tof_tibble, method = c("diffcyt", "glmm", "ttest"), ...)

Arguments

tof_tibble	A 'tof_tbl' or a 'tibble'.
method	A string indicating which statistical method should be used. Valid values include "diffcyt", "lmm", and "ttest".
...	Additional arguments to pass onto the 'tof_analyze_expression_*' function family member corresponding to the chosen method.

Value

A tibble or nested tibble containing the differential abundance results from the chosen method. See tof_analyze_expression_diffcyt, tof_analyze_expression_lmm, and tof_analyze_expression_ttest for details.

See Also

Other differential expression analysis functions: tof_analyze_expression_diffcyt(), tof_analyze_expression_lmm(), tof_analyze_expression_ttest()

Examples

# For differential discovery examples, please see the package vignettes
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keyes-timothy/tidytof documentation built on March 31, 2024, 12:01 p.m.