rmOutliers {Repliscope}

A function to remove outliers from the "score" column of a supplied bed dataframe There are three methods: max, IQR and median. Max is used to remove 1 or more maximum values; IQR uses interquartile range to detect outliers, while median method can be used to remove data based on genome-wide median.

Description

A function to remove outliers from the "score" column of a supplied bed dataframe There are three methods: max, IQR and median. Max is used to remove 1 or more maximum values; IQR uses interquartile range to detect outliers, while median method can be used to remove data based on genome-wide median.

Usage

rmOutliers(bed, method, n = 1, range = 3, loLim = 0.25, hiLim = NULL)

Arguments

bed

A dataframe containing 'score' column (dataframe, required).

method

Method to detect outliers: "max", "IQR" or "median" (string).

n

Number of max values to remove (integer,defaults to 1). Use with "max" method.

range

Number of IQR above the 3rd or below the 1st IQR to set the threshold (double, defaults to 3). Use with "IQR" method.

loLim

Low limit for the median method (double, defaults to 0.25).

hiLim

High limit for the median method (double).

Examples

bedDF <- rmOutliers(W303_S,method="max",n=2) ## removes 2 rows of data containing 3 top values
bedDF <- rmOutliers(W303_S,method="IQR",range=3) ## removes datapoints outside 3 x IQR above the 3rd
 # and below the 1st IQR.
bedDF <- rmOutliers(W303_S,method="median",loLim=0.25,hiLim=2) # removes datapoints that are lower
 # than 0.25 x genome median or above 2 x genome median.