pmartR (version 2.4.6)

RNA_filter: RNA Filter Object

Description

This function returns a RNAFilt object for use with applyFilt

Usage

RNA_filter(omicsData)

Value

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.

Arguments

omicsData

an object of the class 'seqData', created by as.seqData

Author

Rachel Richardson

Details

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.

Examples

if (FALSE) { # requireNamespace("pmartRdata", quietly = TRUE)
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)
}