metaprotr (version 1.2.2)

load_protspeps: load_protspeps

Description

Loads three files: i) peptides abundances expressed as spectral counts, ii) proteins information, and iii) metadata of the mass spectrometry samples. Combines the three files into a "metaproteome_object", a list containing these dataframes.

Usage

load_protspeps(protein_file, peptide_file, metadata_file)

Arguments

protein_file

Character indicating the location of a txt file containing the list of proteins generated in X!TandemPipeline using an adapted iterative approach described by Bassignani, 2019. Separation between columns should be indicated by tabulation. For more details regarding data input check format examples.

peptide_file

Character indicating the location of a txt file containing peptides abundances expressed as spectral counts. This file is generated from X!TandemPipeline using an adapted iterative approach described by Bassignani, 2019. Separation between columns should be indicated by tabulation. For more details regarding data input check format examples.

metadata_file

Character indicating the location of a csv file containing the samples information. The following columns names MUST be present: "SC_name" (sample ids assigned by the user), "msrunfile" (name of samples as indicated in mass spectrometry files and in the columns of peptide_file) and "SampleID" (codes indicating the experimental group). Additional columns containing complementary information can be added by the user (ex. replicates, order of injection, etc.). Separation between columns should be indicated by tabulation. For more details regarding data input check format examples.

Value

A "metaproteome_object", which is a list of six elements containing: 1) dataframe of the protein identifiers, 2) dataframe of the peptide identifiers, 3) dataframe containing the information of peptides with their associated proteins, 4) dataframe of metadata containing the experiment information, 5) dataframe of spectral counts per peptide on each sample, 6) character indicating the type of object generated.

Examples

# NOT RUN {
protein_file <- "location/peptides_abundances.csv"
peptide_file <- "location/proteins_list.csv"
metadata <- "location/metadata.csv"
metaproteome <- load_protspeps(protein_file, peptide_file, metadata_file)

# }