findoutliers | R Documentation |
This functions performs the outlier identification based on the clusters infered with the clustexp
function.
findoutliers(
object,
probthr = 0.001,
outminc = 5,
outlg = 2,
outdistquant = 0.95,
verbose = TRUE
)
object |
|
probthr |
outlier probability threshold for a minimum of |
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 |
SCseq
object with outlier data stored in slot out
and slot outlierpar
. The final clustering partition is stored in
cpart
.
sc <- SCseq(intestinalDataSmall)
sc <- filterdata(sc)
sc <- compdist(sc)
sc <- clustexp(sc)
sc <- findoutliers(sc)
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