Identify potential specialized transduction events on contigs classified as Prophage-like

Search contigs classified as Prophage-like for dense read coverage outside of the pattern-match borders that may indicate specialized transduction. Returns a list with the first object containing a summary table and the second object containing a list of plots of with associated specialzied transduction search results. If the plot is green, it has been identified as having potential specialized transduction.

Usage

specializedTransductionID(
  VLPpileup,
  TrIdentResults,
  specificContig,
  noReadCov = 500,
  specTransLength = 2000,
  matchScoreFilter,
  logScale = FALSE,
  verbose = TRUE,
  SaveFilesTo
)

Arguments

VLPpileup

VLP-fraction pileup file generated by mapping sequencing reads from a sample's ultra-purified VLP-fraction mapped to the sample's whole-community metagenome assembly. The pileup file MUST have the following format: * V1: Contig accession * V2: Mapped read coverage values averaged over 100 bp windows * V3: Starting position (bp) of each 100 bp window. Restarts from 0 at the start of each new contig. * V4: Starting position (bp) of each 100 bp window. Does NOT restart at the start of each new contig.

TrIdentResults

Output from `TrIdentClassifier()`

specificContig

Optional, Search a specific contig classified as Prophage-like ("NODE_1").

noReadCov

Number of basepairs of zero read coverage encountered before specialized transduction searching stops. Default is 500. Must be at least 100.

specTransLength

Number of basepairs of non-zero read coverage needed for specialized transduction to be considered. Default is 2000. Must be at least 100.

matchScoreFilter

Optional, Filter plots using the normalized pattern match-scores. A suggested filtering threshold is provided by `TrIdentClassifier()` if `suggFiltThresh=TRUE`.

logScale

TRUE or FALSE, display VLP-fraction read coverage in log10 scale. Default is FALSE.

verbose

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

SaveFilesTo

Provide a path to the directory you wish to save output to. `specializedTransductionID()` will make a folder within the provided directory to store results.

Value

Large list containing two objects

Examples

data("VLPFractionSamplePileup")
data("TrIdentSampleOutput")

specTransduction <- specializedTransductionID(
  VLPpileup = VLPFractionSamplePileup,
  TrIdentResults = TrIdentSampleOutput
)
#> 2 contigs have potential specialized transduction
#> We recommend that you also view the results of this search with
#>       logScale=TRUE

specTransductionNODE62 <- specializedTransductionID(
  VLPpileup = VLPFractionSamplePileup,
  TrIdentResults = TrIdentSampleOutput,
  specificContig = "NODE_62"
)
#> 1 contigs have potential specialized transduction
#> We recommend that you also view the results of this search with
#>       logScale=TRUE