inst/doc/tapseq_target_genes.R

In TAPseq: Targeted scRNA-seq primer design for TAP-seq

## ---- 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)