iqrxFilter {doseR} | R Documentation

## 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)

[Package doseR version 1.0.0 Index]