patternMatcher {ProActive} | R Documentation |
Controller function for pattern-matching
Description
Creates the pileupSubset, representative of one contig/chunk, used as input for each individual pattern-matching function. After the information associated with the best match for each pattern is obtained, the pattern-match with the lowest mean absolute difference (match-score) is used for classification.
Usage
patternMatcher(
pileup,
windowSize,
minSize,
maxSize,
mode,
minContigLength,
verbose
)
Arguments
pileup |
A .txt file containing mapped sequencing read coverages averaged over 100 bp windows/bins. |
windowSize |
The number of basepairs to average read coverage values over. |
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). |
mode |
Either "genome" or "metagenome". |
minContigLength |
The minimum contig/chunk size (in bp) to perform pattern-matching on. Default is 25000. |
verbose |
TRUE or FALSE. Print progress messages to console. Default is TRUE. |