QC: QC

In kentsisresearchgroup/ProteoModlR: R Suite for Quantitative Proteomics Pathway Modeling

Description

In this quality control function, the data is checked for the presence of all specified columns in the correct order. Data is then filtered to remove peptides without any valid (i.e. < 0) intensity measurement and classified based on the possibility to perform exact or approximate stoichiometry and abundance calculations according to the modification specified by the user (e.g. "phosphorylation" or "acetylation"). The filtered and classified data is exported as a CSV file into the working directory (file name), along with a bar graph summarizing the number of peptides and proteins remaining after each step of quality control.

Usage

QC(data, mod)

Arguments

data

data frame with 12 columns as decribed in documentation.

mod

If any chemoform of a given peptide bears the modification specified in mod="" (f.ex. mod="phosphorylation") all peptides with the same sequence and containing the modification will be classified as Modified, while all peptides with the same sequence and not containing the modification will be classified as Not-Modified. If none of the chemoforms of a peptide contains the specified modification, the peptide is classified Abundance.

Value

data frame of filtered data

Examples

QC(testData,mod="Phosphorylation")

kentsisresearchgroup/ProteoModlR documentation built on May 20, 2019, 9:05 a.m.