createcisTopicObject: Initialize and setup the cisTopic object

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

Initialize and setup the cisTopic object

Description

Initializes the cisTopic object from a counts matrix

Usage

createcisTopicObject(
  count.matrix,
  project.name = "cisTopicProject",
  min.cells = 1,
  min.regions = 1,
  is.acc = 1,
  keepCountsMatrix = TRUE,
  ...
)

Arguments

count.matrix	Count matrix containing cells as columns and regions as rows. The row names must be the coordinates in position format (e.g. chr1:110-610). We recommend to use as input sparse matrices.
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. When using single cell methylation data, this threshold represents the beta value from which above regions will be considered methylated.
keepCountsMatrix	Whether to keep the counts matrix or not inside the object. For large matrices, we recommend to set this to FALSE.
...	Ignored

Details

For single cell methylation data, the input matrix should contain columns as cells, regions as rows and beta values as values instead of counts.

Value

Returns a cisTopic object with the counts data stored in [e-mail]. [e-mail], [e-mail], [e-mail], [e-mail], [e-mail] are also initialized.

Examples

cisTopic_mel <- createcisTopicObject(count.matrix = count.matrix)
cisTopic_mel

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