removeSpots {Spaniel}R Documentation

removeSpots

Description

A function to filter spots from analysis. It requires selectSpots to be run first.

Usage

removeSpots(sObj, pointsToRemove = "points_to_remove.txt")

Arguments

sObj

Either a Seurat object (version 3) or a SingleCellExperiment object containing barcode coordinates in the metadata (Seurat) or colData (SingleCellExperiment).

pointsToRemove

path to points to remove file. Default is "points_to_remove.txt"

Value

A filtered Seurat or SingleCellExperiment Object

Examples

sceObj <- readRDS(file.path(system.file(package = "Spaniel"),
                        "extdata/sceData.rds"))
toRemove <- file.path(system.file(package = "Spaniel"),
                        "points_to_remove.txt")
sceObj_filtered <- removeSpots(sObj = sceObj, pointsToRemove = toRemove)

[Package Spaniel version 1.7.0 Index]