RNA_filter: RNA Filter Object

In pmartR/pmartRqc: Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

RNA Filter Object

Description

This function returns a RNAFilt object for use with applyFilt

Usage

RNA_filter(omicsData)

Arguments

omicsData

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

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.

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.

Author(s)

Rachel Richardson

Examples

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)

pmartR/pmartRqc documentation built on April 25, 2024, 6:18 a.m.