findoutliers {RaceID}

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
)

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.

Value

SCseq object with outlier data stored in slot out and slot outlierpar. The final clustering partition is stored in cpart.

Examples

sc <- SCseq(intestinalDataSmall)
sc <- filterdata(sc)
sc <- compdist(sc)
sc <- clustexp(sc)
sc <- findoutliers(sc)