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

Description Usage Arguments Details Value Author(s) References Examples

View source: R/iqrxFilter.R

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

1
iqrxFilter(se, iqr_multi = 1.5, MEDIAN = FALSE, na.rm = TRUE)

Arguments

se

An s.e. 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 se 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 se object.

Author(s)

AJ Vaestermark, JR Walters.

References

Jue et al. BMC Genomics 2013 14:150

Examples

1
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data(hmel.se)
f_se <- iqrxFilter(se)

avastermark19/doseR_0.99.7 documentation built on May 29, 2019, 8:30 a.m.