#' @export
generate_peptide_table <- function(search_results, sptxt, sample_annotation) {
lib_info <- generate_lib_info(input_sptxt=sptxt)
data <- import_openswath(input_search_results=search_results)
anno <- read_sample_annotation(input_file=sample_annotation)
all_peptides <- long2wide(data, level="PeptideIon")
proteotypic_peptides <- keep_only_proteotypic(all_peptides)
peptides_extend <- merge(proteotypic_peptides, lib_info, by.x="PeptideIon", by.y="PeptideIon")
index_intensity <- which( names(peptides_extend) %in% unique(data$filename) )
peptides_extend_normalized <- normalize_data(peptides_extend, index_intensity)
cons_peptides <- merge_replicates(peptides_extend_normalized, anno)
cons_peptides_long <- wide2long(cons_peptides)
return(cons_peptides_long)
#Wenguang: this will generate a peptide table in "long" format.
}
#' @export
perform_PIN_analysis <- function(peptide_table) {
proteins_long <- pept2prot(peptide_table)
cons_proteins <- long2wide(proteins_long, level="Protein")
semi_cons_peptides_long <- keep_only_semi(peptide_table)
semi_proteins_long <- pept2prot(semi_cons_peptides_long)
semi_cons_proteins <- long2wide(semi_proteins_long, level="Protein")
iPIS <- generate_iPIS_matrix(cons_proteins, semi_cons_proteins)
write_tsv(iPIS)
PIN <- calculate_PIN(iPIS)
write_tsv(PIN)
}
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