calculate_peptide_corr_distr: Calculate peptide correlation between and within peptides of...

In symbioticMe/proBatch: Tools for Diagnostics and Corrections of Batch Effects in Proteomics

Calculate peptide correlation between and within peptides of one protein

Description

Calculate peptide correlation between and within peptides of one protein

Usage

calculate_peptide_corr_distr(data_matrix, peptide_annotation,
  protein_col = "ProteinName", feature_id_col = "peptide_group_label")

Arguments

data_matrix	features (in rows) vs samples (in columns) matrix, with feature IDs in rownames and file/sample names as colnames. See "example_proteome_matrix" for more details (to call the description, use help("example_proteome_matrix"))
peptide_annotation	long format data frame with peptide ID and their corresponding protein and/or gene annotations. See help("example_peptide_annotation").
protein_col	column where protein names are specified
feature_id_col	name of the column with feature/gene/peptide/protein ID used in the long format representation df_long. In the wide formatted representation data_matrix this corresponds to the row names.

Value

dataframe with peptide correlation coefficients that are suggested to use for plotting in plot_peptide_corr_distribution as plot_param:

Examples

selected_genes = c('BOVINE_A1ag','BOVINE_FetuinB','Cyfip1')
gene_filter = example_peptide_annotation$Gene %in% selected_genes
peptides_ann = example_peptide_annotation$peptide_group_label
selected_peptides = peptides_ann[gene_filter]
matrix_test = example_proteome_matrix[selected_peptides,]
pep_annotation_sel = example_peptide_annotation[gene_filter, ]
corr_distribution = calculate_peptide_corr_distr(matrix_test, 
pep_annotation_sel, protein_col = 'Gene')

symbioticMe/proBatch documentation built on April 9, 2023, 11:59 a.m.