Package index • prophosqua

All functions

combined_test_diff_example: Example phosphoproteomics differential expression results
copy_phospho_integration(): copy Markdown and runscript for FragPipe combined_protein.tsv
dea_res_dir(): Get DEA results directory path
dea_xlsx_path(): Get DEA xlsx file path
download_ptmsigdb(): Download PTMsigDB signatures
enrichment_visualization: Enrichment Visualization Functions
exampleN_C_dat: Example dataset exampleN_C_dat
exampleN_C_dat_no_prot: Example dataset exampleN_C_dat_no_prot
explode_multisites(): Explode multisites into individual rows
export_gsea_plots_pdf(): Export GSEA enrichment plots to PDF
extract_gsea_results(): Extract results from clusterProfiler GSEA objects
filter_contaminants(): Filter contaminant proteins from data
filter_significant_sites(): Filter significant PTM sites
get_sequence_windows(): extract sequence windows, from sequence at pos in protein
load_and_preprocess_data(): Load and preprocess DEA data from Excel
make_fasta_summary(): Make FASTA database summary
n_c_integrated_df: Example dataset n_c_integrated_df
n_to_c_expression(): Plot protein and PTM expression
n_to_c_expression_multicontrast(): Plot protein and PTM expression across all contrasts in multi-panel layout
n_to_c_plot(): N to C plot using ggplot2
n_to_c_plot_integrated(): N to C plot for integrated (DPU) results
n_to_c_usage(): Plot PTM occupation, use after adjusting for total proteome
n_to_c_usage_multicontrast(): Plot PTM usage across all contrasts in multi-panel layout
plot_diff_logo(): Plot Difference Sequence Logo (Upregulated - Downregulated)
plot_enrichment_dotplot(): Create enrichment dotplot for top items by FDR
plot_enrichment_heatmap(): Create NES heatmap for top items across contrasts
plot_enrichment_volcano(): Create volcano plot for enrichment results
plot_seqlogo_with_diff(): Plot Sequence Logos with Difference Column
prepare_enrichment_data(): Prepare enrichment data with common computed columns
prepare_gsea_ranks(): Prepare ranked lists for GSEA analysis
prepare_ntoc_data(): Prepare data for N-to-C plotting
ptmsea_data_prep(): Prepare data for PTM-SEA analysis
ptmsea_ora_prep(): Prepare data for PTM-SEA ORA analysis
ptmsigdb_to_term2gene(): Convert PTMsigDB pathways to TERM2GENE format
run_ptmsea(): Run PTM-SEA without direction
run_ptmsea_up_down(): Run directional PTM-SEA analysis
split_ptmsigdb_pathways(): Split PTMsigDB pathways by direction
summarize_enrichment_results(): Create summary table for enrichment results
summarize_significant_sites(): Summarize significant sites by group
test_diff(): Compute MSstats-like test statistics for differential PTM usage
trim_ptmsigdb_pathways(): Trim PTMsigDB pathways to shorter flanking sequences
validate_sequence_window(): Validate sequence window alignment