findoutliers: Inference of outlier cells and final clustering
Description
This functions performs the outlier identification based on the clusters infered with the clustexp function.
Usage
findoutliers(
object,
probthr = 0.001,
outminc = 5,
outlg = 2,
outdistquant = 0.95,
verbose = TRUE
)
Value
SCseq object with outlier data stored in slot out and slot outlierpar. The final clustering partition is stored in
cpart.
Arguments
- object
SCseq class object.
- probthr
outlier probability threshold for a minimum of outlg genes to be an outlier cell. This probability is computed from a negative binomial
background model of expression in a cluster. Default is 0.001.
- outminc
minimal transcript count of a gene in a clusters to be tested for being an outlier gene. Default is 5.
- outlg
Minimum number of outlier genes required for being an outlier cell. Default is 2.
- outdistquant
Real number between zero and one. Outlier cells are merged to outlier clusters if their distance smaller than the outdistquant-quantile of
the distance distribution of pairs of cells in the orginal clusters after outlier removal. Default is 0.95.
- verbose
logical. If FALSE then status output messages are disabled. Default is TRUE.
Examples
Run this codesc <- SCseq(intestinalDataSmall)
sc <- filterdata(sc)
sc <- compdist(sc)
sc <- clustexp(sc)
sc <- findoutliers(sc)
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