simplifyProteins: Simplify Raw Proteins file

In Scavetta/complexomics: Complexome Profiling Analysis package

Simplify Raw Proteins file

Description

• For rows: Keep only one row with highest Precursor Area in cases where for a single Protein Group Accession in a single fraction there are multiple rows with the same combination of Sequence, Mods and Charge

• For cols: remove columns that are not neccessary any more

Usage

simplifyProteins(.data, direction = c("rows", "cols"))

Arguments

.data	a dataframe
direction	character, rows, cols or both

Value

a dataframe

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")
## separate chemical modifications and labelling into separate columns
peptides <- splitModLab(peptides) 
## remove unneccessary columns, simplify rows
peptides <- simplifyProteins(peptides) 

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