createcisTopicObjectFromBAM: Initialize and setup the cisTopic object starting from bam...

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

Initialize and setup the cisTopic object starting from bam files and defined regions

Description

Initializes the cisTopic object from the raw bam files and defined regions

Usage

createcisTopicObjectFromBAM(
  bamfiles,
  regions,
  project.name = "cisTopicProject",
  min.cells = 1,
  min.regions = 1,
  is.acc = 1,
  keepCountsMatrix = TRUE,
  paired = FALSE,
  ...
)

Arguments

bamfiles	List with the paths to the bam files.
regions	Path to the bed file with the defined regions.
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.
paired	Whether data should be treated as paired end or not. If it is FALSE, we count a read if its 5' end falls within the region, if false, fragments will be counted instead of individual reads.
...	See featureCounts function from Rsubread.

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

bamfiles <- c('example_1.bam', 'example_2.bam', 'example_3.bam')
regions <- 'example.bed'
cisTopicObject <- createcisTopicObjectFromBAM(bamfiles, regions)
cisTopicObject

aertslab/cisTopic documentation built on April 6, 2024, 9:31 p.m.