An Improved Function to Perform Regression on Single Cell Data.
Source:R/bb_monocle_regression.R
bb_monocle_regression_better.Rd
This function replaces bb_monocle_regression. It returns log2FoldChange instead of estimates. The log2FoldChange value is the normalized_effect value returned from the monocle regression functions.
Usage
bb_monocle_regression_better(
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.