bb_monocle_regression: A function to perform regression on single cell data.

In blaserlab/blaseRtools: R Tools for Blaser Lab Data Analysis

A function to perform regression on single cell data.

Description

Note: this function is deprecated in favor of bb_monocle_regression_better which returns log2FoldChange instead of estimates. The log2FoldChange value is the normalized_effect value returned from the monocle regression functions.

Usage

bb_monocle_regression(
  cds,
  gene_or_genes,
  stratification_variable = NULL,
  stratification_value = NULL,
  form,
  linking_function = "negbinomial"
)

Arguments

cds	A cell data set object.
gene_or_genes	Genes to regress by.
stratification_variable	Optional colData column to subset the cds by internal to the function.
stratification_value	Optional value to stratify by.
form	The regression formula in the form of "~var1+var2+..."
linking_function	For the generalized linear model.

Value

A tibble containing the regression results.

blaserlab/blaseRtools documentation built on April 14, 2025, 6:04 p.m.