dafsFilter: dafsFilter Function to filter expression data within an...

Description Usage Arguments Details Value Author(s) References Examples

View source: R/dafsFilter.R

Description

This function filters the expression of the supplied object, by invoking the dafsFilter (dafs) function. dafsFilter is a filtering function used to remove rows (genes) of various expression data.

Usage

1

Arguments

se

A SummarizedExperiment object.

PLOT

Boolean, toggles plotting.

Details

This function filters the expression of the supplied object using a Data Adaptive Flag filter. The internal function uses a vector to store Kolmogorov Smirnov distance statistics, loops through cuts of the data to determine targeted K-S statistic, selects data greater than a quantile and runs Mclust on that data to determine theoretical distribution. The wrapper uses simpleFilter to determine first left-most local minima (using the Earth library).

Value

Returns an invisible, filtered SummExp object.

Author(s)

AJ Vaestermark, JR Walters.

References

BMC Bioinformatics, 2014, 15:92

Examples

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library(mclust)
data(hmel.se)
f_se <- dafsFilter(se)

doseR documentation built on May 6, 2019, 3:54 a.m.