selectLocalisedSites {PhosR} | R Documentation |
Select phosphosites with a localisation score higher than the pre-defined probability score (default score = 0.75)
selectLocalisedSites(mat, loc=NULL, prob = 0.75)
mat |
a matrix (or PhosphoExperiment object) with rows corresponding to phosphosites and columns corresponding to samples in replicates for different treatments. |
loc |
a vector of localisation scores |
prob |
a percent from 0 to 1, specifying the localisation probability of quantified values in across all samples for retaining a phosphosite for subsequent analysis. |
a filtered matrix
data('phospho.cells.Ins.pe') ppe <- phospho.cells.Ins.pe ppe_mat <- as.data.frame(SummarizedExperiment::assay(ppe)) # Before filtering dim(ppe) dim(ppe_mat) # Generate arbitrary localisation probabilities for each phosphosite set.seed(2020) localisation_scores <- round(rnorm(nrow(ppe), 0.8, 0.05), 2) table(localisation_scores >= 0.75) # Filter Localisation(ppe) <- localisation_scores ppe_filtered <- selectLocalisedSites(ppe, prob=0.75) ppe_mat_filtered <- selectLocalisedSites(ppe_mat, loc=localisation_scores, prob=0.75) # After filtering dim(ppe_filtered) dim(ppe_mat_filtered)