geneAnnotationSearch {ProActive} | R Documentation |
Search for gene annotations on classified contigs/chunks
Description
Search contigs classified with ProActive for gene-annotations that match a provided key-word(s). Outputs read coverage plots for contigs/chunks with matching annotations.
Usage
geneAnnotationSearch(
ProActiveResults,
pileup,
gffTSV,
geneOrProduct,
keyWords,
inGapOrElev = FALSE,
bpRange = 0,
elevFilter,
saveFilesTo,
verbose = TRUE
)
Arguments
ProActiveResults |
The output from 'ProActive()'. |
pileup |
A .txt file containing mapped sequencing read coverages averaged over 100 bp windows/bins. |
gffTSV |
A .gff file (TSV) containing gene predictions associated with the .fasta file used to generate the pileup. |
geneOrProduct |
"gene" or "product". Search for keyWords associated with genes or gene products. |
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") ) |
inGapOrElev |
TRUE or FALSE. If TRUE, only search for gene-annotations in the gap/elevation region of the pattern-match. Default is FALSE (i.e search the entire contig/chunk for the gene annotation key-words) |
bpRange |
If 'inGapOrElev' = TRUE, the user may specify the region (in base pairs) that should be searched to the left and right of the gap/elevation region. Default is 0. |
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. |
verbose |
TRUE or FALSE. Print progress messages to console. Default is TRUE. |
Value
list of ggplot objects
Examples
geneAnnotMatches <- geneAnnotationSearch(sampleMetagenomeResults, sampleMetagenomePileup,
sampleMetagenomegffTSV, geneOrProduct="product",
keyWords=c("toxin", "drug", "resistance", "phage"))