outlyx: Identify Outliers within Methylumi and Minfi packaged objects

Description Usage Arguments Value Note Author(s) Examples

View source: R/outlyx.R

Description

Seeks to identify outliers based on multiple (currently 2) outlier detection methods for methylumi and minfi packaged objects.

Usage

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outlyx(x, iqr=TRUE, iqrP=2, pc=1,
       mv=TRUE, mvP=0.15, plot=TRUE, ...) 

Arguments

x

A MethyLumiSet, MethylSet, RGChannelSet object or matrix containing raw betas.

iqr

If TRUE, the outliers based on interquartile ranges will be determined

iqrP

The number of interquartile ranges outliers are to be identified from designated principle component.

pc

Desired principal component for outlier identification - only used if other principal components want to be discriminated, only used for IQR outlier detection.

mv

If TRUE, the outliers will detected using pcout

mvP

Arbitrary cut-off point for identifying outliers via pcout

plot

If TRUE, alongside regular output, a plot will be constructed displaying relative 'location' of each sample. Outliers are those that fall within the highlighted regions.

...

Additional arguments passed to pcout

Value

Returns a dataframe of TRUE/FALSE per sample where TRUE is outlying.

Note

May perform poorly on normalized data

Author(s)

Tyler Gorrie-Stone - [email protected]

Examples

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 library(wateRmelon)
 data(melon)
 outliers <- outlyx(melon,iqr=TRUE, iqrP=2, pc=1,
                    mv=TRUE, mvP=0.15, plot=TRUE)

schalkwyk/wateRmelon documentation built on Oct. 27, 2018, 3:26 a.m.