DIscBIO (version 1.1.0)

FindOutliers: Inference of outlier cells

Description

This functions performs the outlier identification for k-means and model-based clustering

Usage

FindOutliers(
  object,
  K,
  outminc = 5,
  outlg = 2,
  probthr = 0.001,
  thr = 2^-(1:40),
  outdistquant = 0.75,
  plot = TRUE,
  quiet = FALSE
)
# S4 method for DISCBIO
FindOutliers(
  object,
  K,
  outminc = 5,
  outlg = 2,
  probthr = 0.001,
  thr = 2^-(1:40),
  outdistquant = 0.75,
  plot = TRUE,
  quiet = FALSE
)

Arguments

object

DISCBIO class object.

K

Number of clusters to be used.

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.

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.

thr

probability values for which the number of outliers is computed in order to plot the dependence of the number of outliers on the probability threshold. Default is 2**-(1:40).set

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 0.75.

plot

if `TRUE`, produces a plot of -log10prob per K

quiet

if `TRUE`, intermediary output is suppressed

Value

A named vector of the genes containing outlying cells and the number of cells on each.

Examples

# NOT RUN {
sc <- DISCBIO(valuesG1msTest)
sc <- Clustexp(sc, cln=2) # K-means clustering
FindOutliers(sc, K=2)

# }