pmartR (version 2.4.6)

total_count_filter: Total Count Filter Object

Description

This function returns a totalcountFilt object for use with applyFilt

Usage

total_count_filter(omicsData)

Value

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.

Arguments

omicsData

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

Author

Rachel Richardson

Details

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).

References

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

Examples

if (FALSE) { # requireNamespace("pmartRdata", quietly = TRUE)
# \donttest{
library(pmartRdata)
to_filter <- total_count_filter(omicsData = rnaseq_object)
summary(to_filter, min_count = 15)
# }
}