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Search for gene annotations on positively classified contigs

Source: R/geneAnnotationSearch.R
geneSearch.Rd

Search contigs classified with TrIdent for gene-annotations that match a provided key-word(s). Outputs read coverage plots for contigs with matching annotations.

Usage

geneSearch(
  TrIdentResults,
  VLPpileup,
  gff,
  searchCol,
  keyWords,
  inPatMat = FALSE,
  bpRange = 0,
  saveFilesTo,
  verbose = TRUE
)

Arguments

TrIdentResults

The output from `TrIdent()`.

VLPpileup

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

gff

A .gff file imported using Bioc.gff::readGFF that is associated with the whole-community contigs

searchCol

The exact column name (in quotes) in the gff file that you'd like to search for specific `keyWords`. Commonly annotation, product, gene, or acc columns, for example, however the specific name may change based on annotation tool used. For example: "pfam_desc".

keyWords

The keyWord(s) to search for. Case independent. Searches will return the string that contains the matching keyWord. KeyWord(s) must be in quotes, comma-separated, and surrounded by c() i.e( c("antibiotic", "resistance", "drug") )

inPatMat

TRUE or FALSE. If TRUE, only search for gene-annotations in the pattern-match region. Default is FALSE (i.e search the entire contig for the gene annotation key-words)

bpRange

If `inPatMat` = TRUE, the user may specify the region (in base pairs) that should be searched to the left and right of the pattern-match region. Default is 0.

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.

verbose

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

Value

list of ggplot objects

Examples

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

patternMatches <- geneSearch(
  TrIdentResults = TrIdentSampleOutput,
  VLPpileup = VLPFractionSamplePileup,
  gff = gffSample,
  searchCol="pfam_desc",
  keyWords=c("toxin", "drug", "resistance", "phage")
)
#> Cleaning pileup file...
#> Searching for matching annotations...
#> 7 contigs have gene annotations that match one or more of the provided keyWords