MSnID-package |
MSnID: Utilities for Handling MS/MS Identifications |
$-method |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
$-method |
The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration. |
$<--method |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
$<--method |
The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration. |
accessions |
Non-redundant list of accession (protein) identifiers |
accessions-method |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
add_mod_symbol |
Annotates peptide sequences with modification symbols |
add_mod_symbol-method |
Annotates peptide sequences with modification symbols |
apply_filter |
Filters the MS/MS identifications |
apply_filter-method |
Filters the MS/MS identifications |
as.numeric-method |
The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration. |
assess_missed_cleavages |
Counts the missing cleavage sites within the peptides sequence |
assess_missed_cleavages-method |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
assess_termini |
Checks if the peptide termini conforms with cleavage specificity |
assess_termini-method |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
class:MSnID |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
class:MSnIDFilter |
The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration. |
coerce-method |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
correct_peak_selection |
Corrects wrong selection of monoisotopic peak |
correct_peak_selection-method |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
c_elegans |
Example mzIdenML File and MSnID Object |
dim-method |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
evaluate_filter |
Filters the MS/MS identifications |
evaluate_filter-method |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
fetch_conversion_table |
Fetches conversion table form one type of identifiers to another |
id_quality |
Identification quality |
id_quality-method |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
infer_parsimonious_accessions |
Eliminates Redundancy in Peptide-to-Protein Mapping |
infer_parsimonious_accessions-method |
Eliminates Redundancy in Peptide-to-Protein Mapping |
length-method |
The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration. |
map_mod_sites |
Maps the modifications to protein sequence |
map_mod_sites-method |
Maps the modifications to protein sequence |
mass_measurement_error |
Computes error of the parent ion mass to charge measurement |
mass_measurement_error-method |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
MSnID |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
MSnID-class |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
MSnIDFilter |
The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration. |
MSnIDFilter-class |
The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration. |
msnidObj |
Example mzIdenML File and MSnID Object |
names-method |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
names-method |
The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration. |
optimize_filter |
Filter criteria optimization to maximize the number of identifications given the FDR upper threshold |
optimize_filter-method |
Filter criteria optimization to maximize the number of identifications given the FDR upper threshold |
peptides |
Non-redundant list of peptides |
peptides-method |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
proteins |
Non-redundant list of accession (protein) identifiers |
proteins-method |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
psms |
Peptide-to-spectrum matches |
psms-method |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
psms<- |
Peptide-to-spectrum matches |
psms<--method |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
read_mzIDs |
Populates MS/MS results table from mzIdentML files |
read_mzIDs-method |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
recalibrate |
Post-experimental recalibration of observed mass to charge ratios |
recalibrate-method |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
remap_accessions |
Changes accessions from one protein id to another |
remap_accessions-method |
Changes accessions from one protein id to another |
remap_fasta_entry_names |
Remapping entries in FASTA file |
report_mods |
Lists modification masses in the MSnID object |
report_mods-method |
Lists modification masses in the MSnID object |
show-method |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
show-method |
The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration. |
update-method |
The "MSnIDFilter" Class for Handling MS/MS Criteria, Relationships and Thresholds for Data Filtration. |
[[-method |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |
[[<--method |
The "MSnID" Class for Mass Spectrometry Based Proteomics Identification Data |