Package 'ProActive'

Title: Detect Elevations and Gaps in Mapped Sequencing Read Coverage
Description: Automate the detection of gaps and elevations in mapped sequencing read coverage using a 2D pattern-matching algorithm. 'ProActive' detects, characterizes and visualizes read coverage patterns in both genomes and metagenomes. Optionally, users may provide gene predictions associated with their genome or metagenome in the form of a .gff file. In this case, 'ProActive' will generate an additional output table containing the gene predictions found within the detected regions of gapped and elevated read coverage.
Authors: Jessie Maier [aut, cre, cph] , Manuel Kleiner [aut, ths]
Maintainer: Jessie Maier <[email protected]>
License: GPL-2
Version: 0.0.2
Built: 2025-01-15 08:39:21 UTC
Source: https://github.com/jlmaier12/proactive

Help Index

Plot results of 'ProActive()' pattern-matching

Description

Plot read coverage of contigs/chunks with detected gaps and elevations and their associated pattern-match.

Usage

plotProActiveResults(pileup, ProActiveResults, elevFilter, saveFilesTo)

Arguments

pileup

A .txt file containing mapped sequencing read coverages averaged over 100 bp windows/bins.
ProActiveResults

The output from 'ProActive()'.
elevFilter

Optional, only plot results with pattern-matches that achieved an elevation ratio (max/min) greater than the specified values. Default is no filter.
saveFilesTo

Optional, Provide a path to the directory you wish to save output to. A folder will be made within the provided directory to store results.

Value

A list containing ggplot objects

Examples

ProActivePlots <- plotProActiveResults(sampleMetagenomePileup,
                                       sampleMetagenomeResults)

Detect elevations and gaps in mapped read coverage patterns.

Description

Performs read coverage pattern-matching and summarizes the results into a list. The first list item summarizes the pattern-matching results. The second list item is the 'cleaned' version of the summary table with all the 'noPattern' classifications removed. (i.e were not filtered out). The third list item contains the pattern-match information needed for pattern-match visualization with 'plotProActiveResults()'. The fourth list item is a table containing all the contigs that were filtered out prior to pattern-matching. The fifth list item contains arguments used during pattern-matching (windowSize, mode, chunkSize, chunkContigs). If the user provides a gffTSV files, then the last list is a table consisting of ORFs found within the detected gaps and elevations in read coverage.

Usage

ProActive(
  pileup,
  mode,
  gffTSV,
  windowSize = 1000,
  chunkContigs = FALSE,
  minSize = 10000,
  maxSize = Inf,
  minContigLength = 30000,
  chunkSize = 1e+05,
  IncludeNoPatterns = FALSE,
  verbose = TRUE,
  saveFilesTo
)

Arguments

pileup

A .txt file containing mapped sequencing read coverages averaged over 100 bp windows/bins.
mode

Either "genome" or "metagenome"
gffTSV

Optional, a .gff file (TSV) containing gene predictions associated with the .fasta file used to generate the pileup.
windowSize

The number of basepairs to average read coverage values over. Options are 100, 200, 500, 1000 ONLY. Default is 1000.
chunkContigs

TRUE or FALSE, If TRUE and 'mode'="metagenome", contigs longer than the ‘chunkSize' will be ’chunked' into smaller subsets and pattern-matching will be performed on each subset. Default is FALSE.
minSize

The minimum size (in bp) of elevation or gap patterns. Default is 10000.
maxSize

The maximum size (in bp) of elevation or gap patterns. Default is NA (i.e. no maximum).
minContigLength

The minimum contig/chunk size (in bp) to perform pattern-matching on. Default is 25000.
chunkSize

If 'mode'="genome" OR if 'mode'="metagenome" and 'chunkContigs'=TRUE, chunk the genome or contigs, respectively, into smaller subsets for pattern-matching. ‘chunkSize' determines the size (in bp) of each ’chunk'. Default is 100000.
IncludeNoPatterns

TRUE or FALSE, If TRUE the noPattern pattern-matches will be included in the ProActive PatternMatches output list. If you would like to visualize the noPattern pattern-matches in 'plotProActiveResults()', this should be set to TRUE.
verbose

TRUE or FALSE. Print progress messages to console. Default is TRUE.
saveFilesTo

Optional, Provide a path to the directory you wish to save output to. A folder will be made within the provided directory to store results.

Value

A list containing 6 objects described in the function description.

Examples

metagenome_results <- ProActive(
  pileup = sampleMetagenomePileup,
  mode = "metagenome",
  gffTSV = sampleMetagenomegffTSV
)