## ---- eval= FALSE---------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly=TRUE)){ # install.packages("BiocManager")} # BiocManager::install("celda") ## ---- eval=TRUE, message=FALSE--------------------------------------------- library(celda) ## -------------------------------------------------------------------------- simCounts <- simulateContaminatedMatrix(G = 300, C = 100, K = 3) ## -------------------------------------------------------------------------- contamination <- simCounts$observedCounts - simCounts$nativeCounts ## -------------------------------------------------------------------------- table(simCounts$z) ## -------------------------------------------------------------------------- colSums(simCounts$phi) colSums(simCounts$eta) ## ---- warning = FALSE, message = FALSE------------------------------------- decontxModel <- decontX(counts = simCounts$observedCounts, z = simCounts$z) ## ---- eval = TRUE, fig.width = 5, fig.height = 5--------------------------- plot(decontxModel$resList$logLikelihood) ## ---- eval = TRUE, fig.width = 5, fig.height = 5--------------------------- plot(decontxModel$resList$estConp, colSums(contamination) / simCounts$NByC, col = simCounts$z) abline(0, 1) ## -------------------------------------------------------------------------- sessionInfo()