sampleMetagenomeResults: sampleMetagenomeResults

In ProActive: Detect Elevations and Gaps in Mapped Sequencing Read Coverage

sampleMetagenomeResults

Description

Output of 'ProActiveDetect()' Report...

Usage

sampleMetagenomeResults

Format

## 'sampleMetagenomeResults' A list with 6 objects:

SummaryTable

A table containing all pattern-matching classifications

CleanSummaryTable

A table containing only gap and elevation pattern-match classifications (i.e. noPattern classifications removed)

PatternMatches

A list object containing information needed to visualize the pattern-matches in 'plotProActiveResults()'

FilteredOut

A table containing contigs/chunks that were filtered out for being too small or having too low read coverage

Arguments

A list object containing arguments used for pattern-matching (windowSize, mode, chunkSize, chunkContigs)

GeneAnnotTable

A table containing gene predictions associated with elevated or gapped regions in pattern-matches

Details

This data was generated by running 'ProActiveDetect()' on the sampleMetagenomePileup and sampleMetagenomegffTSV with default parameters.

ProActive documentation built on April 4, 2025, 12:58 a.m.