API for vladpetyuk/MSnID
Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications

Global functions
$,MSnID-method Man page
$,MSnIDFilter-method Man page
$<-,MSnID-method Man page
$<-,MSnIDFilter-method Man page
.add_mod_symbol Source code
.assess_missed_cleavages Source code
.assess_termini Source code
.check_column Source code
.check_presense_of_flanking_AAs Source code
.compute_accession_coverage Source code
.construct_optimization_grid Source code
.convert_MSnID_to_MSnSet Source code
.get_clean_peptide_sequence Source code
.get_filterString Source code
.get_filterValues Source code
.get_non_AA_characters Source code
.get_num_pep_for_fdr Source code
.id_quality Source code
.is_filterList_valid Source code
.map_mod_sites Source code
.optimize_filter Source code
.optimize_filter.grid Source code
.optimize_filter.grid.mclapply Source code
.optimize_filter.grid.parLapply Source code
.plot_protein_coverage Source code
.read_mzIDs.memoized Source code
.read_mzIDs.mzR Source code
.read_mzIDs.mzR.engine.single.file Source code
.remap_accessions Source code
.strip_flanking_AAs Source code
.strip_modifications_from_peptide Source code
MSnID Man page Source code
MSnID-class Man page
MSnID-package Man page
MSnIDFilter Man page Source code
MSnIDFilter-class Man page
[[,MSnID,ANY,ANY-method Man page
[[,MSnID-method Man page
[[<-,MSnID,ANY,ANY,ANY-method Man page
accessions Man page
accessions,MSnID-method Man page
add_mod_symbol Man page
add_mod_symbol,MSnID-method Man page
apply_filter Man page
apply_filter,MSnID,MSnIDFilter-method Man page
apply_filter,MSnID,character-method Man page
as.numeric,MSnIDFilter-method Man page
assess_missed_cleavages Man page
assess_missed_cleavages,MSnID-method Man page
assess_termini Man page
assess_termini,MSnID-method Man page
c_elegans Man page
class:MSnID Man page
class:MSnIDFilter Man page
coerce,MSnID,MSnSet-method Man page
coerce,MSnID,data.table-method Man page
compute_accession_coverage Man page
compute_accession_coverage,MSnID-method Man page
correct_peak_selection Man page
correct_peak_selection,MSnID-method Man page
dim,MSnID-method Man page
evaluate_filter Man page
evaluate_filter,MSnID-method Man page
extract_sequence_window Man page
extract_sequence_window,MSnID-method Man page
factor_to_str_converter Source code
fetch_conversion_table Man page Source code
get_coverage_for_single_accession Source code
id_quality Man page
id_quality,MSnID-method Man page
infer_parsimonious_accessions Man page
infer_parsimonious_accessions,MSnID-method Man page
length,MSnIDFilter-method Man page
map_mod_sites Man page
map_mod_sites,MSnID-method Man page
map_peptide_position Man page
map_peptide_position,MSnID-method Man page
mass_measurement_error Man page
mass_measurement_error,MSnID-method Man page
msnidObj Man page
names,MSnID-method Man page
names,MSnIDFilter-method Man page
optimize_filter Man page
optimize_filter,MSnIDFilter,MSnID-method Man page
peptides Man page
peptides,MSnID-method Man page
plot_protein_coverage Man page
plot_protein_coverage,MSnID,character-method Man page
proteins Man page
proteins,MSnID-method Man page
psms Man page
psms,MSnID-method Man page
psms<- Man page
psms<-,MSnID,data.frame-method Man page
read_mzIDs Man page
read_mzIDs,MSnID-method Man page
rec_insert Source code
recalibrate Man page
recalibrate,MSnID-method Man page
remap_accessions Man page
remap_accessions,MSnID-method Man page
remap_fasta_entry_names Man page Source code
report_mods Man page
report_mods,MSnID-method Man page
show,MSnID-method Man page
show,MSnIDFilter-method Man page
update,MSnIDFilter-method Man page
vladpetyuk/MSnID documentation built on June 25, 2021, 6:35 a.m.