DetectOutliers: Detect outliers

In Albluca/rRoma: An r implementation of ROMA

Description

Detect outliers

Usage

DetectOutliers(GeneOutDetection, GeneOutThr, ModulePCACenter, CompatibleGenes,
  ExpressionData, PCAType = PCAType, PlotData = FALSE, ModuleName = "",
  PrintInfo = TRUE, Mode = 1, cl = NULL)

Arguments

GeneOutDetection	character scalar, the algorithm used to filter genes in a module. Possible values are 'L1OutVarPerc': percentage variation relative to the median variance explained supporgted by a leave one out approach 'L1OutVarDC': dendrogram clustering statistics on variance explained supported by a leave one out approach 'L1OutExpOut': number of median-absolute-deviations away from median explined variance 'L1OutSdMean': Number of standard deviations away from the mean The option "L1OutExpOut" requires the scater package to be installed.
GeneOutThr	scalar, threshold used by gene filtering algorithm in the modules. It can represent maximum size of filtered cluster ("L1OutVarDC"), minimal percentage variation (L1OutVarPerc) or the number of median-absolute-deviations away from median ("L1OutExpOut")
ModulePCACenter
CompatibleGenes
ExpressionData
PCAType	character string, the type of PCA to perform. It can be "DimensionsAreGenes" or "DimensionsAreSamples"
PlotData
PrintInfo
Mode
cl

Albluca/rRoma documentation built on May 5, 2019, 1:35 p.m.