| Type: | Package |
| Title: | Calculates the Percentage CV for Mass Spectrometry-Based Proteomics Data |
| Version: | 0.4.0 |
| Maintainer: | Alejandro Brenes <abrenes@ed.ac.uk> |
| 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. |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| Imports: | stats |
| RoxygenNote: | 7.3.2 |
| NeedsCompilation: | no |
| Packaged: | 2024-11-21 20:50:51 UTC; ajbrenesmurillo |
| Author: | Alejandro Brenes 
[aut, cre] |
| Repository: | CRAN |
| Date/Publication: | 2024-11-21 21:10:02 UTC |
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)