Statistical & multivariate scores implementation as described Erich et al. (reference below). The scores can be used for systematic evaluation of workflows and comparison of sample preperation methods to check for reproducibility and reliability of the generated data from different preparation protocols.
The devtools package could be used to install msiScores.
install.packages("devtools")
devtools::install_github("CeMOS-Mannheim/msiScores")Note that msiScores was created with renvto help manage R package dependencies and computational reproducibility. for more info, check the renv guide page.
library(msiScores)
data("exampleScores")
test <- getScores(mat, sample(c("1", "2"), nrow(mat), replace = TRUE), compute.r2 = FALSE, compute.fc = FALSE)
Erich, Katrin, et al. "Scores for standardization of on-tissue digestion of formalin-fixed paraffin-embedded tissue in MALDI-MS imaging." Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1865.7 (2017): 907-915.
You are welcome to submit suggestions and bug-reports at: https://github.com/CeMOS-Mannheim/msiScores/issues.
See license document.