This function returns a totalcountFilt object for use with
applyFilt
total_count_filter(omicsData)an object of the class 'seqData', created by
as.seqData
An S3 object of class 'totalcountFilt' (data.frame) that contains the molecule identifier and the total count of observed reads for that molecule across all samples.
Filter is based off of recommendations in edgeR processing, where the low-observed biomolecules are removed from processing. Default recommendation in edgeR is at least 15 total counts observed across samples (i.e., if the sum of counts in a row of e_data is < 15, default edgeR filtering would remove this biomolecule).
Chen Y, Lun ATL, and Smyth, GK (2016). From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. F1000Research 5, 1438. http://f1000research.com/articles/5-1438
# \donttest{
library(pmartRdata)
to_filter <- total_count_filter(omicsData = rnaseq_object)
summary(to_filter, min_count = 15)
# }