simpleFilter: simpleFilter Function to filter expression data of an object.

Description Usage Arguments Details Value Author(s) References Examples

View source: R/simpleFilter.R

Description

simpleFilter is a filtering function used to remove rows (genes) of various expression data.

Usage

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simpleFilter(se, mean_cutoff=NULL, min_cutoff=NULL, median_cutoff=
NULL, counts=TRUE)

Arguments

se

A SummarizedExperiment object.

mean_cutoff

The lower cutoff, using mean.

min_cutoff

The cutoff, expressed as a minimum acceptable value.

median_cutoff

The cutoff, using a median value.

counts

Boolean, use raw counts data (default) or RPKM.

Details

This function filters the expression of the supplied obj.

Value

Returns a filtered SummarizedExperiment object.

Author(s)

AJ Vaestermark, JR Walters.

References

The "doseR" package, 2018 (in press).

Examples

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data(hmel.se) ; f_se <- simpleFilter(se, mean_cutoff=0.5)

doseR documentation built on Nov. 8, 2020, 5:37 p.m.