PerformGlmFit: PerformGlmFit

In bimberlabinternal/CellMembrane: A package with high-level wrappers and pipelines for single-cell RNA-seq tools

PerformGlmFit

Description

Creates an edgeR glm object

Usage

PerformGlmFit(
  seuratObj,
  design,
  test.use = "QLF",
  assayName = "RNA",
  minCountsPerGene = 1,
  legacy = FALSE,
  plotBCV = TRUE
)

Arguments

seuratObj	The seurat object
design	The model.matrix object
test.use	Can be either QLF or LRT. QLF runs edgeR::glmQLFTest, while LRT runs edgeR::glmLRT
assayName	The name of the assay to use
minCountsPerGene	Any genes with fewer than this many counts (across samples) will be dropped.
legacy	A passthrough variable for edgeR's glmQLF function. They recently (R 4.0) changed the default behavior, so this will break on earlier versions of R.
plotBCV	A boolean determining if the BCV plot should be shown.

Value

An edgeR glm object

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