quantFilter: quantFilter Function to filter expression data of a...

In WaltersLab/doseR: doseR

quantFilter Function to filter expression data of a SummarizedExperiment object.

Description

This function filters the expression of the supplied object; quantFilter is a filtering function used to remove rows (genes) of various expression data.

Usage

quantFilter (se, lo.bound=.25, hi.bound=.75, MEDIAN = FALSE,
na.rm = TRUE)

Arguments

se	A SummarizedExperiment object.
lo.bound	The lower cutoff, expressed as a percentage.
hi.bound	The upper cutoff, expressed as a percentage.
MEDIAN	Boolean, Calculate RowMeans or RowMedians.
na.rm	Boolean, NA removal.

Details

This function filters the expression of the supplied object, based on a selected percentage cutoff.

Value

Returns a filtered SummarizedExperiment object.

Author(s)

AJ Vaestermark, JR Walters.

References

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

Examples

data(hmel.se)
f_se <- quantFilter(se, lo.bound=0.5)

WaltersLab/doseR documentation built on June 24, 2024, 2:51 a.m.