## ----install_MEM,eval = FALSE------------------------------------------------- # # if (!require("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("cytoMEM") # ## ----PBMC_data,eval=TRUE------------------------------------------------------ library(cytoMEM) data(PBMC) head(PBMC) ## ----MEM,eval=TRUE------------------------------------------------------------ MEM_values <- MEM( PBMC, transform = TRUE, cofactor = 15, # Change choose.markers to TRUE to see and select channels in console choose.markers = FALSE, markers = "all", choose.ref = FALSE, zero.ref = FALSE, # Change rename.markers to TRUE to see and choose new names for channels in console rename.markers = FALSE, new.marker.names = "none", IQR.thresh = NULL ) str(MEM_values) ## ----build_heatmaps,eval=TRUE------------------------------------------------- build_heatmaps( MEM_values, cluster.MEM = "both", cluster.medians = "none", cluster.IQRs = "none", display.thresh = 1, output.files = FALSE, labels = FALSE, only.MEMheatmap = FALSE) ## ----RMSD, eval=TRUE---------------------------------------------------------- #data(MEM_matrix) MEM_RMSD( MEM_values[[5]][[1]], format=NULL, output.matrix=FALSE) ## ----eval=TRUE---------------------------------------------------------------- sessionInfo()