iqrxFilter: iqrxFilter Function to filter expression data within a...
In avastermark19/doseR_0.99.4: doseR

Description Usage Arguments Details Value Author(s) References Examples

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

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

`cD`	A countDat 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.

This function filters the expression of the supplied cD 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 countDat object.

AJ Vaestermark, JR Walters.

Jue et al. BMC Genomics 2013 14:150

data(hmel.data.doser)
reps <- c("Male", "Male", "Male", "Female", "Female", "Female")
annotxn <- data.frame("Chromosome" = factor(hmel.dat$chromosome,
levels = 1:21))
hm.tr<-hmel.dat$trxLength
hm<-new("countDat",data=hmel.dat$readcounts,seglens=hm.tr,
annotation=annotxn)
replicates(hm) <- reps
libsizes(hm) <- getLibsizes2(hm, estimationType = "total")
rpkm(hm) <- make_RPKM(hm)
f_hm <- iqrxFilter(hm)