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

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

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')

proBatch documentation built on Nov. 8, 2020, 4:55 p.m.