create_peptide_annotation: Prepare peptide annotation from long format data frame Create...

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

Description

Prepare peptide annotation from long format data frame

Create light-weight peptide annotation data frame for selection of illustrative proteins

Usage

create_peptide_annotation(
  df_long,
  feature_id_col = "peptide_group_label",
  protein_col = c("ProteinName", "Gene")
)

Arguments

df_long	data frame where each row is a single feature in a single sample. It minimally has a sample_id_col, a feature_id_col and a measure_col, but usually also an m_score (in OpenSWATH output result file). See help("example_proteome") for more details.
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.
protein_col	column where protein names are specified

Value

data frame containing petpide annotations

See Also

plot_peptides_of_one_protein, plot_protein_corrplot

Examples

generated_peptide_annotation <- create_peptide_annotation(
example_proteome, feature_id_col = "peptide_group_label",
protein_col = c("Protein"))

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