CalculateCutOff: Calculate cut-off value

In lyc-1995/MySeuratWrappers: My extentions to Seurat package

Description

Compute cut-off for outliars of an given feature.

Usage

CalculateCutOff(object, ...)

## Default S3 method:
CalculateCutOff(
  object,
  metrics = c("mean", "median"),
  n.dev = 3,
  cut.off.end = c("paired", "lower", "higher"),
  cut.off.given = NULL,
  cut.off.given.only = FALSE,
  ...
)

## S3 method for class 'Seurat'
CalculateCutOff(
  object,
  assay = NULL,
  feature = NULL,
  cells = NULL,
  slot = NULL,
  ...
)

Arguments

object	An object
...	Arguments passed to other methods
metrics	Default is 'mean', and standard deviation will be used as discrete parameter. Median absolute deviation will be used for 'median' as metrics
n.dev	Number for discrete parameter
cut.off.end	Default is paired-end. Can set with 'lower' or 'higher' end
cut.off.given	Add extra cut-off values
cut.off.given.only	Whether or not to use the given cut-offs only, default is FALSE
assay	Which assay to use
feature	Which feature to calculate. Must be from either rownames of Seurat data or colnames of meta.data
cells	Which cells to use. Default is all cells
slot	Which slot to use. Default is counts slot

Value

Returns a vector storing cut-off(s) for outliars

lyc-1995/MySeuratWrappers documentation built on June 30, 2020, 11:48 a.m.