createcisTopicObjectFrom10X: Initialize and setup the cisTopic object starting from...

View source: R/InitializecisTopic.R

createcisTopicObjectFrom10XR Documentation

Initialize and setup the cisTopic object starting from CellRanger ATAC output files and defined regions

Description

Initializes the cisTopic object from CellRanger ATAC output files and defined regions.

Usage

createcisTopicObjectFrom10X(
  fragments,
  regions,
  metrics,
  project.name = "cisTopicProject",
  min.cells = 1,
  min.regions = 1,
  is.acc = 1,
  keepCountsMatrix = TRUE,
  ...
)

Arguments

fragments

Fragment file from CellRanger ATAC (/outs/fragments.tsv.gz)

regions

Path to the bed file with the defined regions.

metrics

List of CellRanger barcodes and their metrics (/outs/singlecell.csv)

project.name

Project name (string).

min.cells

Minimal number of cells in which the region has to be accessible. By default, all regions accessible in at least one cell are kept.

min.regions

Minimal number of regions that have to be accessible within a cell to be kept. By default, all cells with at least one region accessible are kept.

is.acc

Number of counts necessary to consider a region as accessible.

keepCountsMatrix

Whether to keep the counts matrix or not inside the object. For large matrices, we recommend to set this to FALSE.

Value

Returns a cisTopic object with the counts data stored in object@count.matrix. object@binary.count.matrix, object@cell.names, object@cell.data (including counting statistics), object@regions.ranges, object@regions.data are also initialized.

Examples

fragments <- '/outs/fragments.tsv.gz'
regions <- '/outs/peaks.bed'
metrics <- '/outs/singlecell.csv'
cisTopicObject <- createcisTopicObjectFrom10X(fragments, regions, metrics)
cisTopicObject

aertslab/cisTopic documentation built on June 1, 2022, 2 a.m.