cytogroup {CytoGLMM} | R Documentation |
Group-specific fixed effects model
cytogroup( df_samples_subset, protein_names, condition, group = "donor", cell_n_min = Inf, cell_n_subsample = 0 )
df_samples_subset |
Data frame or tibble with proteins counts, cell condition, and group information |
protein_names |
A vector of column names of protein to use in the analysis |
condition |
The column name of the condition variable |
group |
The column name of the group variable |
cell_n_min |
Remove samples that are below this cell counts threshold |
cell_n_subsample |
Subsample samples to have this maximum cell count |
A list of class cytoglm
containing
groupfit |
|
df_samples_subset |
possibly subsampled df_samples_subset table |
protein_names |
input protein names |
condition |
input condition variable |
group |
input group names |
cell_n_min |
input cell_n_min |
cell_n_subsample |
input cell_n_subsample |
set.seed(23) df <- generate_data() protein_names <- names(df)[3:12] df <- dplyr::mutate_at(df, protein_names, function(x) asinh(x/5)) group_fit <- CytoGLMM::cytogroup(df, protein_names = protein_names, condition = "condition", group = "donor") group_fit