iqrxFilter: iqrxFilter Function to filter expression data within an s.e....

In WaltersLab/doseR: doseR

iqrxFilter Function to filter expression data within an s.e. object.

Description

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

Usage

iqrxFilter(se, iqr_multi = 1.5, MEDIAN = FALSE, na.rm = TRUE)

Arguments

se	A SummarizedExperiment object.
iqr_multi	Numeric multiplier; removes any outliers that are iqr_multi times the mid-50 percentile distance greater or less than the 25th and 75th percentiles, by default
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 and selected interquartile range multiplier. The function iqrxFilter will: 1) log-base two transform all RPKM values (obligatory); (2) remove any outliers that were 1.5 times the mid-50 percentile distance greater or less than the 75th and 25th percentiles (by default), respectively; and (3) uses mean values and instead of median values (by default).

Value

Returns a filtered SummarizedExperiment object.

Author(s)

AJ Vaestermark, JR Walters.

References

Jue et al. BMC Genomics 2013 14:150

Examples

data(hmel.se)
f_se <- iqrxFilter(se)

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