## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("SUITOR") ## ----------------------------------------------------------------------------- library(SUITOR) ## ----------------------------------------------------------------------------- data(SimData, package="SUITOR") dim(SimData) SimData[1:6, 1:6] ## ----table1, echo=FALSE------------------------------------------------------- v1 <- c("min.value", "min.rank", "max.rank", "k.fold", "em.eps", "max.iter", "n.starts", "get.summary", "plot", "print") v2 <- c("Minimum value of matrix before factorizing", "Minimum rank", "Maximum rank", "Number of folds", "EM algorithm stopping tolerance", "Maximum number of iterations in EM algorithm", "Number of starting points", "0 or 1 to create summary results", "0 or 1 to produce an error plot", "0 or 1 to print info (0=no printing)") v3 <- c("1e-4", "1", "10", "10", "1e-5", "2000", "30", "1", "1", "1") tab1 <- data.frame(Name=v1, Description=v2, "Default Value"=v3, stringsAsFactors=FALSE, check.names=FALSE) knitr::kable(tab1) ## ----------------------------------------------------------------------------- OP <- list(max.rank=3, k.fold=5, n.starts=4) set.seed(123) re <- suitor(SimData, op=OP) str(re) ## ----table2, echo=FALSE------------------------------------------------------- v1 <- c("min.value", "n.starts", "print") v2 <- c("Minimum value of matrix before factorizing", "Number of starting points", "0 or 1 to print info (0=no printing)") v3 <- c("1e-4", "30", "1") tab2 <- data.frame(Name=v1, Description=v2, "Default Value"=v3, stringsAsFactors=FALSE, check.names=FALSE) knitr::kable(tab2) ## ----------------------------------------------------------------------------- re$rank set.seed(123) Extract <- suitorExtractWH(SimData, re$rank) head(Extract$W) Extract$H[,1:3] ## ----------------------------------------------------------------------------- suppressPackageStartupMessages(library(MutationalPatterns)) COSMIC <- get_known_signatures(source = "COSMIC_v3.2") plot_96_profile(Extract$W, condensed=TRUE, ymax=0.3) CS <- cos_sim_matrix(Extract$W, COSMIC) CS[, 1:3] ## ----------------------------------------------------------------------------- sessionInfo()