A function to perform regression on single cell data.
Source:R/bb_monocle_regression.R
bb_monocle_regression.Rd
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.