This function returns a RNAFilt object for use with
applyFilt
RNA_filter(omicsData)an object of the class 'seqData', created by
as.seqData
An S3 object of class 'RNAFilt' (data.frame) that contains the sample identifiers, library size, the number of unique biomolecules with non-zero observations per sample, and the proportion of non-zero observations over the total number of biomolecules.
Filter omicsData samples by library size (number of reads) or number of unique non-zero biomolecules per sample. Useful for visualizing if a sample contains lower than expected number of reads.
library(pmartRdata)
to_filter <- RNA_filter(omicsData = rnaseq_object)
summary(to_filter, size_library = 10000)
summary(to_filter, min_nonzero = 5000)
summary(to_filter, min_nonzero = .2)