findNCGs: Get negative control genes from each batch of the data

In DavisLaboratory/standR: Spatial transcriptome analyses of Nanostring's DSP data in R

Get negative control genes from each batch of the data

Description

Get negative control genes from each batch of the data

Usage

findNCGs(spe, n_assay = 2, batch_name = "SlideName", top_n = 200)

Arguments

spe	A Spatial Experiment object.
n_assay	Integer to indicate the nth count table in the assay(spe) to be used.
batch_name	Column name indicating batches.
top_n	Integer indicate how many genes to be included as negative control genes.

Value

A Spatial Experiment object, conatining negative control genes in the metadata.

Examples

data("dkd_spe_subset")

spe <- findNCGs(dkd_spe_subset, top_n = 100)
S4Vectors::metadata(spe)$NCGs

DavisLaboratory/standR documentation built on Sept. 8, 2024, 9:57 p.m.