# Expression Weighted Celltype Enrichment

## Documentation for package ‘EWCE’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

add_res_to_merging_list | Add to results to merging list
bin_columns_into_quantiles | bin_columns_into_quantiles
bin_specificity_into_quantiles | bin_specificity_into_quantiles
bootstrap_enrichment_test | Bootstrap celltype enrichment test
check_ewce_genelist_inputs | check_ewce_genelist_inputs
controlled_geneset_enrichment | Celltype controlled geneset enrichment
convert_new_ewce_to_old | convert_new_ewce_to_old
convert_old_ewce_to_new | convert_old_ewce_to_new
drop_uninformative_genes | drop_uninformative_genes
ewce_expression_data | Bootstrap celltype enrichment test for transcriptome data
ewce_plot | Plot EWCE results
filter_genes_without_1to1_homolog | filter_genes_without_1to1_homolog
fix_bad_hgnc_symbols | fix_bad_hgnc_symbols - Given an expression matrix, wherein the rows are supposed to be HGNC symbols, find those symbols which are not official HGNC symbols, then correct them if possible. Return the expression matrix with corrected symbols.
fix_bad_mgi_symbols | fix_bad_mgi_symbols - Given an expression matrix, wherein the rows are supposed to be MGI symbols, find those symbols which are not official MGI symbols, then check in the MGI synonm database for whether they match to a proper MGI symbol. Where a symbol is found to be an aliases for a gene that is already in the dataset, the combined reads are summed together.
generate_bootstrap_plots | Generate bootstrap plots
generate_bootstrap_plots_for_transcriptome | Generate bootstrap plots
generate_celltype_data | generate_celltype_data
generate_controlled_bootstrap_geneset | generate_controlled_bootstrap_geneset
get_celltype_table | get_celltype_table
get_summed_proportions | Get summed proportions
merged_ewce | Multiple EWCE results from multiple studies
merge_two_expfiles | merge_two_expfiles
prepare_genesize_control_network | Prepare genesize control network
prep_dendro | prep_dendro