makeBackgroundFeather: makeBackgroundFeather
In aertslab/cisTopic: cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
makeBackgroundFeather R Documentation
makeBackgroundFeather
Description
Create a background cisTarget ranking out of the genome-wide cisTarget regions based on given regions.
Usage
makeBackgroundFeather(
pathToFeather,
subsetRegions = NULL,
subsetMotifs = NULL,
pathToSave,
...
)
Arguments
pathToFeather
Path to the feather database to use. Note that this database has to match the genome used for mapping.
subsetRegions
Subset of regions to be re-ranked (optional).
subsetMotifs
Subset of motifs to be used from the database (optional).
pathToSave
Path to save background database.
...
See RcisTarget
Details
The created database can be used as input for topicsRcisTarget(); using reduced_database = TRUE. Subsetting by
regions and motifs is optional, but at least one of them as to be filled.
Value
A file containing the feather database.
Examples
pathToFeather <- "hg19-regions-1M-9species.all_regions.mc9nr.feather"
subsetRegion <- cisTopicObject@region.data$CtxLabels
pathToSave <- "hg19-regions-subsetMelanoma.feather"
makeBackgroundFeather(pathToFeather, subsetRegion, pathToSave)
aertslab/cisTopic documentation built on April 6, 2024, 9:31 p.m.
R Package Documentation
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| makeBackgroundFeather | R Documentation |
makeBackgroundFeather
Description
Create a background cisTarget ranking out of the genome-wide cisTarget regions based on given regions.
Usage
makeBackgroundFeather(
pathToFeather,
subsetRegions = NULL,
subsetMotifs = NULL,
pathToSave,
...
)
Arguments
pathToFeather |
Path to the feather database to use. Note that this database has to match the genome used for mapping. |
subsetRegions |
Subset of regions to be re-ranked (optional). |
subsetMotifs |
Subset of motifs to be used from the database (optional). |
pathToSave |
Path to save background database. |
... |
See RcisTarget |
Details
The created database can be used as input for topicsRcisTarget(); using reduced_database = TRUE. Subsetting by
regions and motifs is optional, but at least one of them as to be filled.
Value
A file containing the feather database.
Examples
pathToFeather <- "hg19-regions-1M-9species.all_regions.mc9nr.feather"
subsetRegion <- cisTopicObject@region.data$CtxLabels
pathToSave <- "hg19-regions-subsetMelanoma.feather"
makeBackgroundFeather(pathToFeather, subsetRegion, pathToSave)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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