Man pages for CambridgeCentreForProteomics/camprotR
Processing, analysing and visualising CCP proteomics data
| add_peptide_positions | Add a column describing the position(s) of the peptide... |
| add_PTM_positions | Add a column describing the position(s) of the PTM(s) with... |
| add_site_sequence | Add a column with amino acid sequence around a PTM |
| append_fasta | Append sequences to end of a FASTA |
| camprotR-package | camprotR: Processing, analysing and visualising CCP... |
| center_normalise_to_ref | Center-median normalise the expression matrix in an MSnSet... |
| check_uniprot_release | Check the current UniProt release |
| compare_IDs | Identify the proportion of exact matches in protein IDs |
| compare_sequences_per_protein | Compare the number of peptides per protein pre/post-consensus... |
| compare_single_master | Identify the proportion of peptides with a single assigned... |
| count_features_per_protein | Count the number of features (rows) per protein |
| dep_gene2cat | GO terms assigned to proteins in DEP results |
| dep_results | Results table from DEP package |
| determine_ancestor_function | Determine GO ancestor object |
| determine_offspring_function | Determine GO offspring object |
| download_ccp_crap | Download CCP cRAP FASTA file |
| estimate_go_overrep | Estimate effect size of GO over-representation |
| estimate_incorporation | Estimate SILAC (2-plex) incorporation rate from PD output |
| expand_terms | Expand data.frame GO terms |
| filter_TMT_PSMs | Filter a PSM-level MSnSet to remove low quality PSMs |
| get_all_mappings | Get all mappings for GO terms |
| get_ancestor_go | Get all ancestor GO terms |
| get_cat_palette | Generate a colour-blind friendly palette for categorical... |
| get_ccp_crap | Get the UniProt sequences in CCP cRAP |
| get_enriched_go | GO term enrichment using goseq |
| get_incorporation | Determine SILAC (2-plex) incorporation rate given intensity... |
| get_medians | Extract the expression matrix column medians from an MSnSet |
| get_notch_per_protein | Summarise the number of sub-notch PSM intensities per protein |
| get_parsimony_pep2prot | Identify the consensus peptide to master protein mapping... |
| get_psm_metrics | Summarise percentage of tag intensities below a given... |
| get_psm_silac_mod_regex | Get a pre-defined regex for a SILAC modification in PSM... |
| get_ratio | Get ratio of two numbers |
| get_sequence | Get the amino acid sequence around a PTM |
| get_sequence2protein | Approximate parsimony approach to map sequence to protein... |
| lfq_oops_rnase_pep | PeptideGroups PD output for LFQ of RNase +/- OOPS experiment |
| lfq_oops_rnase_psm | PSM PD output for LFQ of RNase +/- OOPS experiment |
| make_fasta | Make a FASTA using UniProt accessions |
| match_proteins | Check if two protein IDs are the same allowing for: 1.... |
| parse_features | Parse Proteome Discoverer output |
| parse_PTM_scores | Parse the PTM probabilities and add new columns with PTM... |
| pep_oops_1 | PeptideGroups PD output for SILAC labelled U-2 OS cells |
| pep_oops_2 | PeptideGroups PD output for SILAC labelled U-2 OS cells |
| pep_oops_3 | PeptideGroups PD output for SILAC labelled U-2 OS cells |
| pep_oops_4 | PeptideGroups PD output for SILAC labelled U-2 OS cells |
| pep_silac_p0 | PeptideGroups PD output for SILAC labelled MOLM-13 cells |
| pep_silac_p4 | PeptideGroups PD output for SILAC labelled MOLM-13 cells |
| plot_below_notch_per_prot | Plot the number of sub-notch PSM intensities per protein |
| plot_fraction_below_notch_per_prot | Plot the fraction of sub-notch PSM intensities per protein |
| plot_go | Plot selected GO terms |
| plot_incorporation | Plot annotated histogram of incorporation values |
| plot_missing_SN | Plot the missing values vs signal:noise |
| plot_missing_SN_per_sample | Plot the missing values vs signal:noise for each sample |
| plot_quant | Plot distributions for feature intensities per sample. |
| plot_TMT_notch | Plot histograms for TMT tag intensities including notch... |
| psm_oops_1 | PSM PD output for SILAC labelled U-2 OS cells |
| psm_oops_2 | PSM PD output for SILAC labelled U-2 OS cells |
| psm_oops_3 | PSM PD output for SILAC labelled U-2 OS cells |
| psm_oops_4 | PSM PD output for SILAC labelled U-2 OS cells |
| psm_silac_p4 | PSMs PD output for SILAC labelled MOLM-13 cells |
| psm_tmt_phospho | PSM-level PD output for phospho TMT10-plex data |
| psm_tmt_total | PSM-level PD output for total proteome TMT10-plex data |
| psm_to_peptide_style_modifications | Transformes PSM-level Modifications annotation style to... |
| read_infiles | Extract sequence:protein ID mappings |
| remove_dots | Remove duplicated full stops |
| remove_redundant_go | Remove redundant GO terms |
| remove_silac_modifications | Remove SILAC labels from modifications |
| remove_x | Remove leading X |
| restrict_features_per_protein | Remove features which are assigned to a protein with too few... |
| silac_psm_seq_int | Extract peptide sequencing and interference information from... |
| sub_crap | Insert cRAP numbers into a character vector |
| theme_camprot | ggplot theme for package |
| theme_csd | Charlotte's ggplot2 theme |
| update_average_sn | Adds new feature describing the average reporter Signal/Noise... |
