DATATABLE_AnnotateProteotypic: DATAFRAME_AnnotateProteotypic Since we observe that some...

In 47Lies/isoformnspectRe: Companion package of a nextflow pipeline

Description

DATAFRAME_AnnotateProteotypic Since we observe that some proteins are not present in the Proteins field, we decieded to

Usage

DATATABLE_AnnotateProteotypic(PeptideDataFrame, ProteinBank, Threads = 1)

Arguments

PeptideDataFrame	MaxQuant peptide search as a data frame
ProteinBank	AAStringSet of the protein fasta file that was used for the mass spectrometry analysis
Threads	Number of parallel sessions (numeric)

Value

PeptideDataFrame Updated data frame with informations

Examples

library(isoformnspectRe)
ProteinBankFastaFilePath <- system.file("extdata",
"protein_bank.example.fasta",
package = "isoformnspectRe")
ProteinBank <- Biostrings::readAAStringSet(ProteinBankFastaFilePath)
PeptidePath <- system.file("extdata",
                           "peptides.example.txt",
                           package = "isoformnspectRe")
options(datatable.integer64 = "numeric")
Peptides <- data.table::fread(PeptidePath, sep = "\t")
DATATABLE_AnnotateProteotypic(Peptides, ProteinBank, Threads = 1)

47Lies/isoformnspectRe documentation built on May 29, 2021, 3 p.m.