## ---- results = 'hide'-----------------------------------------------------
library(MAST)

knitr::opts_chunk$set(message = FALSE,error = FALSE,warning = FALSE)
data(maits, package='MAST')
unlog <- function(x) ceiling(2^x - 1)
sca_raw =  FromMatrix(t(maits$expressionmat), maits$cdat, maits$fdat)
assays(sca_raw)$counts = unlog(assay(sca_raw))
assayNames(sca_raw)

## ----scaterQC,results='hide'-----------------------------------------------
library(scater)
sca_raw = calculateQCMetrics(sca_raw)
plotRowData(sca_raw, x = 'log10_mean_counts', 'pct_dropout_by_counts')
plotColData(sca_raw, y="total_features_by_counts", x="total_counts")

## --------------------------------------------------------------------------
sca_raw <- runPCA(sca_raw, ncomponents=5, exprs_values = 'et')
plotReducedDim(sca_raw, use_dimred = 'PCA', colour_by = 'condition')

## --------------------------------------------------------------------------
data(sc_example_counts)