removeSpots: removeSpots

In Spaniel: Spatial Transcriptomics Analysis

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

seuratObj <- readRDS(file.path(system.file(package = "Spaniel"),
                        "extdata/SeuratData.rds"))
toRemove <- file.path(system.file(package = "Spaniel"),
                        "points_to_remove.txt")
sObjFiltered <- removeSpots(sObj = seuratObj, pointsToRemove = toRemove)

Spaniel documentation built on Nov. 8, 2020, 5:54 p.m.