## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", crop = NULL ) ## ----vignetteSetup, echo=FALSE, message=FALSE, warning = FALSE---------------- ## Track time spent on making the vignette startTime <- Sys.time() ## ----"install", eval = FALSE-------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) { # install.packages("BiocManager") # } # # BiocManager::install("CTSV", version = "devel") # # ## Check that you have a valid Bioconductor installation # BiocManager::valid() ## ----library packages,results = 'hide'---------------------------------------- suppressPackageStartupMessages(library(CTSV)) suppressPackageStartupMessages(library(SpatialExperiment)) ## ----ST----------------------------------------------------------------------- data("CTSVexample_data", package="CTSV") spe <- CTSVexample_data[[1]] W <- CTSVexample_data[[2]] gamma_true <- CTSVexample_data[[3]] Y <- assay(spe) # dimension of bulk ST data dim(Y) # dimension of cell-type proportion matrix: dim(W) # SV genes in each cell type: colnames(Y)[which(gamma_true[,1] == 1)] colnames(Y)[which(gamma_true[,2] == 1)] # Number of SV genes at the aggregated level: sum(rowSums(gamma_true)>0) ## ----Run CTSV----------------------------------------------------------------- result <- CTSV(spe,W,num_core = 8) ## ----results------------------------------------------------------------------ # View on q-value matrix head(result$qval) ## ----SVgenes------------------------------------------------------------------ re <- svGene(result$qval,0.05) # SV genes in each cell type: re$SVGene ## ----session information------------------------------------------------------ sessionInfo()