## ----eval=FALSE---------------------------------------------------------- # # try http:// if https:// URLs are not supported # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("iteremoval") ## ------------------------------------------------------------------------ library(iteremoval) # input two datasets removal.stat <- feature_removal(SWRG1, SWRG0, cutoff1=0.95, cutoff0=0.95, offset=c(0.25, 0.5, 2, 4)) ## ----eval=TRUE----------------------------------------------------------- # input SummarizedExperiment object removal.stat <- feature_removal(SummarizedData, SummarizedData$Group==0, cutoff1=0.95, cutoff0=0.95, offset=c(0.25, 0.5, 2, 4)) ## ----echo=TRUE----------------------------------------------------------- ggiteration_trace(removal.stat) + theme_bw() ## ----echo=TRUE----------------------------------------------------------- features <- feature_prevalence(removal.stat, index=255, hist.plot=TRUE) features ## ----echo=TRUE----------------------------------------------------------- feature_screen(features, prevalence=4)