cleanData {ComPrAn} | R Documentation

## 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 pp451@cam.ac.uk

Rick Scavetta office@scavetta.academy

### 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")

[Package ComPrAn version 1.2.0 Index]