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

In aertslab/cisTopic: cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data

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 [e-mail]. [e-mail], [e-mail], [e-mail] (including counting statistics), [e-mail], [e-mail] 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 April 6, 2024, 9:31 p.m.