## ----options, include=FALSE, echo=FALSE--------------------------------------- library(BiocStyle) knitr::opts_chunk$set(warning=FALSE, error=FALSE, message=FALSE) ## ----construct1--------------------------------------------------------------- library(LoomExperiment) counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10) sce <- SingleCellExperiment(assays = list(counts = counts)) scle <- SingleCellLoomExperiment(sce) ## OR scle <- LoomExperiment(sce) ## ----construct2--------------------------------------------------------------- scle <- SingleCellLoomExperiment(assays = list(counts = counts)) ## ----coerce------------------------------------------------------------------- scle <- as(sce, "SingleCellLoomExperiment") scle ## ----load_l1------------------------------------------------------------------ l1_file <- system.file("extdata", "L1_DRG_20_example.loom", package = "LoomExperiment") scle <- import(l1_file, type="SingleCellLoomExperiment") scle ## ----construct_LoomGraph------------------------------------------------------ a <- c(1, 2, 3) b <- c(3, 2, 1) w <- c(100, 10, 1) df <- DataFrame(a, b, w) lg <- as(df, "LoomGraph") ## OR lg <- LoomGraph(a, b, weight = w) lg ## ----subset_LoomGraph--------------------------------------------------------- lg[c(1, 2)] lg[-c(2)] ## ----construct_LoomGraphs----------------------------------------------------- lgs <- LoomGraphs(lg, lg) names(lgs) <- c('lg1', 'lg2') lgs ## ----get_col_row_graphs------------------------------------------------------- colGraphs(scle) rowGraphs(scle) ## ----replace_LoomGraphs------------------------------------------------------- colGraphs(scle) <- lgs rowGraphs(scle) <- lgs colGraphs(scle) rowGraphs(scle) colGraphs(scle)[[1]] rowGraphs(scle)[[1]] ## ----subset_LoomExperiment---------------------------------------------------- scle2 <- scle[c(1, 3), 1:2] colGraphs(scle2)[[1]] rowGraphs(scle2)[[1]] ## ----rbind_LoomExperiment----------------------------------------------------- scle3 <- rbind(scle, scle) scle3 colGraphs(scle3) rowGraphs(scle3) colGraphs(scle3)[[1]] rowGraphs(scle3)[[1]] ## ----export_LoomExperiment---------------------------------------------------- temp <- tempfile(fileext='.loom') export(scle2, temp) ## ----------------------------------------------------------------------------- sessionInfo()