Function reference • PlexedPiper

All functions

best_PTM_location_by_ascore(): Improve Phosphosite Localization

compute_num_peptides_per_1000aa(): Compute number of peptides per 1000 aa

create_crosstab(): Makes Cross-Tab With Quantitative Data.

create_msnset(): Makes MSnSet from Quantitative Crosstab.

filter_masic_data(): Filtering MASIC Data

filter_msfragger_data(): Filtering MSFragger Data

filter_msgf_data() filter_msgf_data_peptide_level() filter_msgf_data_protein_level() filter_msgf_data_SiteID_level(): Filtering MSGF Data

filter_msgf_data_missed_cleavages(): Filtering MSGF Data

make_rii_peptide_gl() make_results_ratio_gl() make_rii_peptide_ph() make_results_ratio_ph() assess_redundant_protein_matches() assess_noninferable_proteins(): Format Tables for BIC

read_AScore_results(): Read AScore results from folder

read_masic_data(): Reading MASIC Results. Generic.

read_msgf_data(): Reading MS-GF+ Results. Generic.

read_study_design(): Utilities for reading study design files.

remap_accessions_refseq_to_gene() remap_accessions_uniprot_to_gene(): Remap accessions

remap_accessions_refseq_to_gene_fasta() remap_accessions_uniprot_to_gene_fasta(): Remap Sequence IDs in FASTA File

reporter_converter: Converter for TMT Reporter Channels

run_plexedpiper(): Wrapper for PlexedPiper