PerformDifferentialExpression: PerformDifferentialExpression

View source: R/PseudoBulk.R

PerformDifferentialExpressionR Documentation

PerformDifferentialExpression

Description

This is designed to perform DE using edgeR on a pseudobulked seurat object

Usage

PerformDifferentialExpression(
  fit,
  contrast,
  contrast_name,
  logFC_threshold = 1,
  FDR_threshold = 0.05,
  test.use = "QLF",
  showPlots = T
)

Arguments

fit

The glm fit object generated by PerformGlmFit

contrast

The contrast, passed directly to edgeR::glmQLFTest or edgeR::glmLRT

contrast_name

A name for the contrast

logFC_threshold

The min logFC

FDR_threshold

The min FDR to report

test.use

Can be either QLF or LRT. QLF runs edgeR::glmQLFTest, while LRT runs edgeR::glmLRT

showPlots

Boolean determining if the volcano plots and p value dsitributions should be shown.

Value

A list with the differential_expression results, volcano ggplot object and pvalue_dist ggplot object


bimberlabinternal/CellMembrane documentation built on Dec. 25, 2024, 8:10 a.m.