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

In WaltersLab/doseR: doseR

dafsFilter Function to filter expression data within an object.

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

dafsFilter(se, PLOT=TRUE)

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

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

WaltersLab/doseR documentation built on March 2, 2023, 7:01 p.m.