createcisTopicObjectFromMeth: 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 methylation files

Description

Initializes the cisTopic object from DNA methylation calls. These files must be tab separated files containing chromosome, position, number of methylated reads and total number of reads.

Usage

createcisTopicObjectFromMeth(
  methfiles,
  regions,
  project.name = "cisTopicProject",
  min.cells = 1,
  min.regions = 1,
  is.acc = 0.5,
  ...
)

Arguments

methfiles	List with the paths to the tab separated files containing the methylation information.
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	Minimal beta value to be considered methylated. As default, it is 0.5.
...	Ignored

Value

Returns a cisTopic object with the counts data (in this case, beta values data) stored in [e-mail]. NA's are filled as 0's. [e-mail], [e-mail], [e-mail] (including counting statistics), [e-mail], [e-mail] are also initialized.

Examples

methfiles <- c('meth_1.txt', 'meth_2.txt', 'meth_3.txt')
regions <- 'example.bed'
cisTopicObject <- createcisTopicObjectFromBAM(methfiles, regions)
cisTopicObject

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