lmc.lola.plots.tables: lmc.lola.plots.tables

In lutsik/MeDeCom: Decomposition of heterogeneous methylomes

lmc.lola.plots.tables

Description

This functions calls lmc.lola.enrichment and returns plots representing those results, as well as the tables with LOLA enrichment results.

Usage

lmc.lola.plots.tables(
  medecom.result,
  annotation.filter = NULL,
  anno.data,
  K = NULL,
  lambda = NULL,
  cg_subset = NULL,
  diff.threshold = 0.5,
  region.type = "ensembleRegBuildBPall",
  temp.dir = tempdir(),
  type = "hypo",
  assembly = "hg19",
  lola.db = NULL,
  ...
)

Arguments

medecom.result	An object of type MeDeComSet-class or the location of an .RData file, where such an object is stored.
annotation.filter	A numeric vector specifying the sites that have been removed from rnb.set in a preprocessing step (e.g. coverage filtering) or a path to an .RData file.
anno.data	The original RnBSet-class object containing methylation, sample meta and annotation information, a path to a directory stored by save.rnb.set or a data.frame containing CpG annotations (ann_C)
K	The number of LMCs specified for the MeDeCom run.
lambda	The lambda parameter selected.
cg_subset	The index of the selection strategy employed (e.g. most variable CpGs).
diff.threshold	The difference cutoff between median methylation in the remaining LMCs and the LMC of interest used to call a CpG differentially methylated. The higher this value, the more conservative the selection.
region.type	Region type used to annotate CpGs to potentially regulatory regions (see https://rnbeads.org/regions.html) for a list of available region types.
temp.dir	Path to a directory used to store temporary files.
type	Which direction is to be tested for enrichment. Can be one of "hypo", "hyper", or "differential"
assembly	The assembly used. Needs to be one of "hg19", "hg38" or "mm10". Does not need to be specified, if rnb.set is a RnBSet-class
lola.db	A loaded LOLA database as loaded with LOLA::loadRegionDB. If this value is NULL, the database is loaded automatically and stored in the temporary directory.
...	Further arguments passed to lmc.lola.enrichment

Value

A list with two elements, one of them containing the plots for each LMC and the other for the corresponding LOLA enrichment tables

Author(s)

Michael Scherer

See Also

lmc.lola.enrichment

lutsik/MeDeCom documentation built on July 15, 2024, 4:51 a.m.