iqrxFilter: iqrxFilter Function to filter expression data within a...
In avastermark19/doseR_development: Test Package of doseR

Description Usage Arguments Details Value Author(s) References

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

1	iqrxFilter(cD, perc_cutoff=0.25, perc_cutoff2=0.25, IQR_MULTIPLIER=1.5, MEDIAN=FALSE)

`cD`	A countData object.
`perc_cutoff`	The lower cutoff, expressed as a percentage.
`perc_cutoff2`	The upper cutoff, expressed as a percentage.
`IQR_MULTIPLIER`	Numeric multiplier; removes any outliers that are IQR_MULTIPLIER times the mid-50 percentile distance greater or less than the perc_cutoff and 1-perc_cutoff2 (25th and 75th percentiles, by default)
`MEDIAN`	Boolean, Calculate RowMeans or RowMedians.

This function filters the expression of the supplied countData 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).

Returns a filtered countData object.

AJ Vaestermark, JR Walters.

Jue et al. BMC Genomics201314:150

avastermark19/doseR_development documentation built on May 6, 2019, 4:31 p.m.