Package 'proteomicsCV'

Title: Calculates the Percentage CV for Mass Spectrometry-Based Proteomics Data
Description: Calculates the percentage coefficient of variation (CV) for mass spectrometry-based proteomic data. The CV can be calculated with the traditional formula for raw (non log transformed) intensity data, or log transformed data.
Authors: Alejandro Brenes [aut, cre]
Maintainer: Alejandro Brenes <[email protected]>
License: MIT + file LICENSE
Version: 0.4.0
Built: 2024-11-25 16:24:31 UTC
Source: CRAN

Help Index

protLogCV protCV

Description

Calculates the percentage CV for intensity based proteomic data.

Usage

protLogCV(logData, base)
protCV(data)

Arguments

data

input dataframe of the intensity values.

logData

input dataframe of the log transformed intensity values.

base

numerical base of the logarithm that was used to transform the data. Values that are accepted are 2 (for log2) and 10 (for log10)

Value

returns a list containing the percentage CVs

Author(s)

Alejandro J. Brenes

References

https://www.biorxiv.org/content/10.1101/2024.09.11.612398v1

Examples

library(proteomicsCV)
log_intensity_df<-data.frame(intensity1=c(16.93157,26.57542,19.90749,18.86056),
                         intensity2=c(17.16546,27.77706,19.45854,19.60721),
                         intensity3=c(17.04260,27.21697,19.70314,16.19530),
                         intensity4=c(17.08473,26.99766,17.93342,17.97693))

# log formula with the data already transformed to log2
cvs<-protLogCV(log_intensity_df, 2)
# log formula with the data not log transformed
not_log_intensity_df<-data.frame(intensity1=c(125000,100000000,983450,475987),
                         intensity2=c(147000,230000000,720450,798656),
                         intensity3=c(135000,156000000,853566,75036),
                         intensity4=c(139000,134000000,250321,257986))
# base formula with raw intensity (no log transformation)
raw_cvs<-protCV(not_log_intensity_df)