Function reference • camprotR

All functions
`add_PTM_positions()`	Add a column describing the position(s) of the PTM(s) with respect to the protein
`add_peptide_positions()`	Add a column describing the position(s) of the peptide sequence with respect to the protein
`add_site_sequence()`	Add a column with amino acid sequence around a PTM
`append_fasta()`	Append sequences to end of a FASTA
`center_normalise_to_ref()`	Center-median normalise the expression matrix in an MSnSet using medians from a reference dataset
`check_uniprot_release()`	Check the current UniProt release
`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
`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
`filter_TMT_PSMs()` `filter_TMT_PSMs()`	Filter a PSM-level MSnSet to remove low quality PSMs
`get_ancestor_go()`	Get all ancestor GO terms
`get_cat_palette()`	Generate a colour-blind friendly palette for categorical colour encoding
`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 values for Light and Heavy
`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 across multiple runs
`get_psm_metrics()`	Summarise percentage of tag intensities below a given threshold and missing
`get_psm_silac_mod_regex()`	Get a pre-defined regex for a SILAC modification in PSM format
`get_ratio()`	Get ratio of two numbers
`get_sequence()`	Get the amino acid sequence around a PTM
`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
`parse_PTM_scores()`	Parse the PTM probabilities and add new columns with PTM information
`parse_features()`	Parse Proteome Discoverer output
`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_TMT_notch()`	Plot histograms for TMT tag intensities including notch annotation
`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.
`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 peptide-level style
`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 supporting features in total
`silac_psm_seq_int()`	Extract peptide sequencing and interference information from SILAC PSM-level output
`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 ratio.

Reference

All functions