examples/ex_checkClusterability.R

In prostarproteomics/DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

data(Exp1_R25_prot, package="DAPARdata")
obj <- Exp1_R25_prot[seq_len(100)]
level <- 'protein'
metacell.mask <- match.metacell(GetMetacell(obj), c("Missing POV", "Missing MEC"), level)
indices <- GetIndices_WholeMatrix(metacell.mask, op = ">=", th = 1)
obj <- MetaCellFiltering(obj, indices, cmd = "delete")
averaged_means <- averageIntensities(obj$new)
only_means <- dplyr::select_if(averaged_means, is.numeric)
only_features <- dplyr::select_if(averaged_means, is.character)
means <- purrr::map(purrr::array_branch(as.matrix(only_means), 1), mean)
centered <- only_means - unlist(means)
centered_means <- dplyr::bind_cols(
feature = dplyr::as_tibble(only_features),
dplyr::as_tibble(centered))
checkClust <- checkClusterability(centered_means, b = 100)