GPsInElevGaps: Detect gene predictions in elevations and gaps
In ProActive: Detect Elevations and Gaps in Mapped Sequencing Read Coverage

GPsInElevGaps

R Documentation

Detect gene predictions in elevations and gaps

Extracts subsets of the gffTSV associated with gene predictions that fall within regions of detected gapped or elevated read coverage.

GPsInElevGaps(
  elevGapSummList,
  windowSize,
  gffTSV,
  mode,
  chunkContigs,
  chunkSize
)

`elevGapSummList`	A list containing pattern-match information associated with all elevation and gap classifications. (i.e. no NoPattern classifications)
`windowSize`	The number of basepairs to average read coverage values over. Options are 100, 200, 500, 1000 ONLY. Default is 1000.
`gffTSV`	Optional, a .gff file (TSV) containing gene predictions associated with the .fasta file used to generate the pileup.
`mode`	Either "genome" or "metagenome"
`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.
`chunkSize`	If 'mode'="genome" OR if 'mode'="metagenome" and 'chunkContigs'=TRUE, chunk the genome or contigs, respectively, into smaller subsets for pattern-matching.