msqrobLm {msqrob2} | R Documentation |
Low-level function for parameter estimation with msqrob using the ordinary least squares or robust regression base on the MASS::rlm function.
msqrobLm(y, formula, data, robust = TRUE, maxitRob = 5)
y |
A |
formula |
Model formula. The model is built based on the covariates in the data object. |
data |
A |
robust |
|
maxitRob |
|
A list of objects of the StatModel
class.
Lieven Clement, Oliver M. Crook
# Load example data # The data are a Feature object with containing # a SummarizedExperiment named "peptide" with MaxQuant peptide intensities # The data are a subset of spike-in the human-ecoli study # The variable condition in the colData of the Feature object # contains information on the spike in condition a-e (from low to high) data(pe) # Aggregate peptide intensities in protein expression values pe <- aggregateFeatures(pe, i = "peptide", fcol = "Proteins", name = "protein") pe # Fit MSqrob model using robust regression with the MASS rlm function models <- msqrobLm(assay(pe[["protein"]]), ~condition, colData(pe)) #' getCoef(models[[1]])