## ---- include = FALSE--------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ---- message=FALSE, results="hide"------------------------------------------- library(TAPseq) library(Seurat) # example of mouse bone marrow 10x gene expression data data("bone_marrow_genex") # transcript counts GetAssayData(bone_marrow_genex)[1:10, 1:10] # number of cells per cell type table(Idents(bone_marrow_genex)) ## ---- message=FALSE, results="hide"------------------------------------------- # automatically select a number of target genes using 10-fold cross-validation target_genes_cv <- selectTargetGenes(bone_marrow_genex) head(target_genes_cv) length(target_genes_cv) ## ---- message=FALSE, results="hide"------------------------------------------- # identify approximately 100 target genes that can be used to identify cell populations target_genes_100 <- selectTargetGenes(bone_marrow_genex, targets = 100) length(target_genes_100) ## ---- message=FALSE, warning=FALSE, fig.height=3, fig.width=7.15-------------- plotTargetGenes(bone_marrow_genex, target_genes = target_genes_100)