topicsRcisTarget | R Documentation |
Run RcisTarget in the binarized topics
topicsRcisTarget(
object,
genome,
pathToDb,
reduced_database = FALSE,
nesThreshold = 3,
rocthr = 0.005,
maxRank = 20000,
nCores = 1,
...
)
object |
Initialized cisTopic object, after the object@binarized.regions.to.Rct has been filled. |
genome |
Genome to which the data was aligned or liftovered (hg19, mm9, dm3 or dm6). |
pathToDb |
Path to the feather or parquet database to use. Note that this database has to match the genome used for mapping. |
reduced_database |
Whether a reduced version of the database (e.g. background database) is being used or not (by default, it is set to false). |
nesThreshold |
Minimum enrichment score that a motif should have to be included in the table |
rocthr |
ROC threshold for AUC calculation. For mouse and human, we recommend 0.005; for fly, 0.01. |
maxRank |
Number of regions consider for visualization. For mouse and human, we recommend 20000; for fly, 5000. |
... |
See RcisTarget |
Motif enrichment table is stored in object@binarized.RcisTarget
pathToDb <- "hg19-regions-1M-9species.all_regions.mc9nr.feather"
cisTopicObject <- topicRcisTarget(cisTopicObject, genome='hg19', pathToDb)
cisTopicObject
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