coefficient_table | R Documentation |
Extracts a table of coefficients from a tibble containing model objects. It tests whether each coefficient differs significantly from zero under the Wald test and adjusts the p-values for multiple hypothesis testing using the method of Benjamini and Hochberg, placing these adjusted values in the q-value column.
coefficient_table(model_tbl)
model_tbl |
A tibble of model objects, generally the output of
|
A table of coefficient data for each gene.
cell_metadata <- readRDS(system.file('extdata', 'worm_embryo/worm_embryo_coldata.rds', package='monocle3')) gene_metadata <- readRDS(system.file('extdata', 'worm_embryo/worm_embryo_rowdata.rds', package='monocle3')) expression_matrix <- readRDS(system.file('extdata', 'worm_embryo/worm_embryo_expression_matrix.rds', package='monocle3')) cds <- new_cell_data_set(expression_data=expression_matrix, cell_metadata=cell_metadata, gene_metadata=gene_metadata) cds <- preprocess_cds(cds, num_dim=50) cds <- align_cds(cds, alignment_group = "batch", residual_model_formula_str = "~ bg.300.loading + bg.400.loading + bg.500.1.loading + bg.500.2.loading + bg.r17.loading + bg.b01.loading + bg.b02.loading") cds <- reduce_dimension(cds) ciliated_genes <- c("che-1", "hlh-17", "nhr-6", "dmd-6", "ceh-36", "ham-1") cds_subset <- cds[rowData(cds)$gene_short_name %in% ciliated_genes,] gene_fits <- fit_models(cds_subset, model_formula_str = "~embryo.time") fit_coefs <- coefficient_table(gene_fits)
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