buildCellTypeIndex: Builds an 'SCFind' object from a 'SingleCellExperiment'...

In hemberg-lab/scfind: A search tool for single cell RNA-seq data by gene lists

Builds an SCFind object from a SingleCellExperiment object

Description

This function will index a SingleCellExperiment as an SCFind index.

Usage

buildCellTypeIndex.SCESet(sce, dataset.name, assay.name = "counts",
  cell.type.label = "cell_type1", qb = 2)

## S4 method for signature 'SingleCellExperiment'
buildCellTypeIndex(sce,
  dataset.name = "", assay.name = "counts",
  cell.type.label = "cell_type1", qb = 2)

Arguments

sce	object of SingleCellExperiment class
dataset.name	name of the dataset that will be prepended in each cell_type
assay.name	name of the SingleCellExperiment assay that will be considered for the generation of the index
cell.type.label	the cell.type metadata of the colData SingleCellExperiment that will be used for the index
qb	number of bits per cell that are going to be used for quantile compression of the expression data

Value

an SCFind object

hemberg-lab/scfind documentation built on March 27, 2022, 8:56 p.m.