metaprotr (version 1.2.2)

getsc_specific: getsc_specific

Description

Returns the abundances, expressed as spectral counts (SC), of the different peptides, subgroups (also referred as metaprotein) or groups within the samples of the experiment. The abundance corresponds to the sum of SC of the specific peptides present in a given subgroup or group. See X!TandemPipeline for more details concerning the grouping algorithm.

Usage

getsc_specific(metaproteome_object, type_SCspecific)

Arguments

metaproteome_object

List defined as "metaproteome_object" with dataframes having a similar format to that generated from "load_protspeps" function. It contains metaproteomics data such as peptide and protein abundances and sample information.

type_SCspecific

Character indicating the type of data to be returned. The possible options are: i) "sc_specific_peptides" for peptides, or ii) "sc_groups" for groups, or iii) "sc_subgroups" for subgroups. For more details of the identification algorithm (peptides, subgroups, groups) check X!TandemPipeline.

Value

A list of four elements defined as "spectral_count_object". The first element is a dataframe organized in function of peptides OR subgroups (also referred as metaproteins) OR groups. The entities of this dataframe have their abundance expressed as SC from specific peptides. The second element is a dataframe of metadata containing the experiment information. The third element is a dataframe containing the information of peptides with their associated proteins. The fourth element is a character indicating the type of object generated.

Examples

# NOT RUN {
# From a given "metaproteome_object" add the taxonomic classification

metaproteome <- load_protspeps(proteins_file, peptides_file, metadata_file)
metaproteome_taxo <- add_taxonomy(metaproteome, meta99_full_taxo) 

# Organize proteomics data by peptides OR subgroups OR groups

SC_specific_peptides <- getsc_specific(metaproteome_taxo, 'sc_specific_peptides') 
SC_specific_groups <- getsc_specific(metaproteome_taxo, 'sc_groups') 
SC_specific_subgroups <- getsc_specific(metaproteome_taxo, 'sc_subgroups') 

# }