Package index • biomasslmb

All functions

add_filter_ptm_pos_rowdata_mq(): Add rowData columns with positions of PTMs with respect to peptide sequence

add_gene_long_protein_name_pd(): Extract the gene name and long-form protein name from the master protein descriptions column

add_independent_filtering_padj(): Perform independent filtering to threshold the over-representation testing on the number of features in each category to limit the multiple testing burden

add_peptide_positions(): Add a column describing the position of the peptide sequence with respect to the protein

add_peptide_positions_from_cleavage(): Add peptide positions with respect to the protein

add_ptm_pos_rowdata_mq(): Add rowData columns with positions of PTMs with respect to peptide sequence

add_ptm_positions(): Add rowData columns with details of PTMs positions

add_tm_info(): Add transmembrane domain details

add_topology_info(): Add topology details

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

create_long_form_imputed_data(): Create long format data with column defining if quantification value is imputed

dia_qf: DIA data

estimate_overrep(): Estimate effect size of over-representation

filter_TMT_PSMs(): Filter a PSM-level summarizedExperiment to remove low quality PSMs

filter_by_protein_fdr(): Filter to remove peptides from proteins failing the protein FDR threshold

filter_features_diann(): Filter DIA-NN output

filter_features_mq_dda(): Filter MaxQuant DDA output

filter_features_pd_dda(): Filter Proteome Discoverer DDA output

filter_features_per_protein(): Remove features which are assigned to a protein with too few supporting features in total

filter_features_sn(): Filter Spectronaut output

filter_maxquant_ptm(): Filter PTM data from MaxQuant to retain those with a given PTM

get_ancestor_go(): Get all ancestor GO terms

get_cat_palette(): Generate a colour-blind friendly palette for categorical colour encoding

get_crap_fasta_accessions(): Extract the contaminants protein accessions from a cRAP fasta file

get_enriched_go(): GO term enrichment using goseq

get_go_terms(): Obtain GO term annotations for proteins

get_maxquant_cont_accessions(): Extract the contaminants protein accessions from a MaxQuant contaminants fasta file

get_medians(): Extract the assay column medians from an MSnSet

get_n_feature_per_prot(): Identify how many features (PSMs/Peptides) are quantified for each protein

get_protein_no_quant_mask(): Identify proteins which have too few features to quantify protein abundance in each sample

get_protein_tm_topology(): Obtain protein transmembrane-domains and topology information

get_samples_present(): Extract the number of samples each feature was detected in for each experiment in a Qfeatures object

make_fasta(): Make a FASTA using UniProt accessions

make_unique_all(): Make Elements of a Character Vector Unique (Numbering From 1)

mask_protein_level_quant(): Replace protein-level quantifications with NA if they derive from too few lower feature level quantifications

parse_PTM_scores_pd(): Parse the PTM probabilities from Proteome Discoverer and add new columns with PTM information

plot_cor_samples(): Plot the correlation between sample

plot_go(): Plot selected GO terms

plot_go_terms_upset(): Plot selected GO terms

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_missing_upset(): Plot the most common missing value patterns

plot_pca(): Create a Principle Component plot from the feature quantification

plot_protein_assays(): Plot quantification at multiple levels

plot_quant(): Plot distributions for feature intensities per sample.

plot_rt_dist(): Plot the retention time distribution

plot_rt_vs_delta(): Plot the retention time vs delta precursor mass

plot_samples_present(): Plots the number of samples each feature was detected in for each experiment in a Qfeatures object

plot_volcano(): Volcano plot for differential abundance testing

psm_tmt_total: PSM-level PD output for total proteome TMT10-plex data

query_protein_tm_topology(): Query UniProt to determine protein transmembrane-domains and topology

readDIANNFilterQJoin(): Read in data from DIA-NN

remove_dots(): Remove duplicated full stops

remove_redundant_go(): Remove redundant GO terms

remove_redundant_psm_quant(): Remove redundant Peptide Spectrum Matches

remove_x(): Remove leading X

restrict_imputation(): Restrict imputed values to specific conditions

sub_crap(): Insert cRAP numbers into a character vector

theme_biomasslmb(): A ggplot2 theme for the package

tmt_qf: TMT data

update_average_sn(): Adds new feature describing the average reporter Signal/Noise ratio.

update_peptide_assignments(): Update PSM level protein/master protein assignments using peptide-level assignments