## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( echo = TRUE, collapse = TRUE, comment = "#>" ) ## ----Installation from Bioconductor, eval = FALSE----------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("scRecover") ## ----Developmental version from Bioconductor, eval = FALSE-------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("scRecover", version = "devel") ## ----Installation from GitHub, eval = FALSE----------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("miaozhun/scRecover") ## ----Load scRecover, eval = TRUE---------------------------------------------- library(scRecover) library(BiocParallel) suppressMessages(library(SingleCellExperiment)) ## ----Load scRecoverTest------------------------------------------------------- data(scRecoverTest) ## ----counts------------------------------------------------------------------- dim(counts) counts[1:6, 1:6] ## ----labels------------------------------------------------------------------- length(labels) table(labels) ## ----oneCell------------------------------------------------------------------ head(oneCell) length(oneCell) ## ----demo1, eval = TRUE------------------------------------------------------- # Load test data for scRecover data(scRecoverTest) # Run scRecover with Kcluster specified scRecover(counts = counts, Kcluster = 2, outputDir = "./outDir_scRecover/", verbose = FALSE) # Or run scRecover with labels specified # scRecover(counts = counts, labels = labels, outputDir = "./outDir_scRecover/") ## ----demo2, eval = TRUE------------------------------------------------------- # Load test data for scRecover data(scRecoverTest) # Convert the test data in scRecover to SingleCellExperiment data representation sce <- SingleCellExperiment(assays = list(counts = as.matrix(counts))) # Run scRecover with SingleCellExperiment input sce (Kcluster specified) scRecover(counts = sce, Kcluster = 2, outputDir = "./outDir_scRecover/", verbose = FALSE) # Or run scRecover with SingleCellExperiment input sce (labels specified) # scRecover(counts = sce, labels = labels, outputDir = "./outDir_scRecover/") ## ----demo3, eval = TRUE------------------------------------------------------- # Load test data data(scRecoverTest) # Downsample 10% read counts in oneCell set.seed(999) oneCell.down <- countsSampling(counts = oneCell, fraction = 0.1) # Count the groundtruth dropout gene number in the downsampled cell sum(oneCell.down == 0 & oneCell != 0) # Estimate the dropout gene number in the downsampled cell by estDropoutNum estDropoutNum(sample = oneCell.down, depth = 10, return = "dropoutNum") ## ----demo4, eval = FALSE------------------------------------------------------ # # Run scRecover with Kcluster specified # scRecover(counts = counts, Kcluster = 2, parallel = TRUE) # # # Run scRecover with labels specified # scRecover(counts = counts, labels = labels, parallel = TRUE) ## ----demo5, eval = FALSE------------------------------------------------------ # # Set the parameters and register the back-end to be used # param <- MulticoreParam(workers = 18, progressbar = TRUE) # register(param) # # # Run scRecover with 18 cores (Kcluster specified) # scRecover(counts = counts, Kcluster = 2, parallel = TRUE, BPPARAM = param) # # # Run scRecover with 18 cores (labels specified) # scRecover(counts = counts, labels = labels, parallel = TRUE, BPPARAM = param) ## ----demo6, eval = FALSE------------------------------------------------------ # # Set the parameters and register the back-end to be used # param <- SnowParam(workers = 8, type = "SOCK", progressbar = TRUE) # register(param) # # # Run scRecover with 8 cores (Kcluster specified) # scRecover(counts = counts, Kcluster = 2, parallel = TRUE, BPPARAM = param) # # # Run scRecover with 8 cores (labels specified) # scRecover(counts = counts, labels = labels, parallel = TRUE, BPPARAM = param) ## ----help, eval = FALSE------------------------------------------------------- # # Documentation for scRecover # ?scRecover # # # Documentation for estDropoutNum # ?estDropoutNum # # # Documentation for countsSampling # ?countsSampling # # # Documentation for normalization # ?normalization # # # Documentation for test data # ?scRecoverTest # ?counts # ?labels # ?oneCell ## ----sessionInfo-------------------------------------------------------------- sessionInfo()