LoomExperiment.R
In LoomExperiment: LoomExperiment container

## ----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()