dafsFilter {doseR} | R Documentation

## 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)

[Package doseR version 1.10.0 Index]