cleanData: Clean raw peptide complexomics data

In Scavetta/complexomics: Complexome Profiling Analysis package

Clean raw peptide complexomics data

Description

Perform initial, mandatory, cleaning of data Function to process raw input data into format required for subsequent analysis. .data is a data frame containing raw input data. This function checks (not neccessarily in this order):

• renames Sequence ID column to Fraction and converts values in this column from letters to numbers

• reorders Protein Group Accessions containing multiple proteins

• removes rows in which PSM Ambiguity == 'Rejected'

• removes rows in which # Protein Groups == 0

• removes rows in which Precursor Area is NA

• removes cols that are not used at all

Usage

cleanData(.data, fCol = "Search ID")

Arguments

.data	dataframe
fCol	character The column containing the fractions, e.g. "Search ID" (default)

Value

dataframe

Author(s)

Petra Palenikova [e-mail]

Rick Scavetta [e-mail]

Examples

 
##Use example peptide data set, read in and clean data
inputFile <- system.file("extData", "data.txt", package = "ComPrAn")
peptides <- peptideImport(inputFile)
peptides <- cleanData(peptides, fCol = "Search ID")

Scavetta/complexomics documentation built on Oct. 1, 2022, 2:15 a.m.