chimera: Detect chimeras
In lerch-a/Rvsearch: R vsearch Wrapper

Description Usage Arguments Examples

Detect chimeras de novo and using a reference database.

  chimeraDetectionDenovo(filename, 
                         abskew=2.0, mindiffs=3L, mindiv=0.8, minh=0.28,
                         nonchimeras=sub(".fasta", "_nonchimera.fasta", filename), 
                         chimeras=sub(".fasta", "_chimera.fasta", filename), 
                         borderline=sub(".fasta", "_bordchimera.fasta", filename), 
                         uchimeout=sub(".fasta", "_chimeraResults.txt", filename))

`filename`	Input file
`abskew`	Minimum abundance ratio of parent vs chimera (2.0)
`mindiffs`	Minimum number of differences in segment (3)
`mindiv`	Minimum divergence from closest parent (0.8)
`minh`	Minimum score (0.28)
`borderline`	Output borderline chimeric sequences to file
`chimeras`	Output chimeric sequences to file
`nonchimeras`	Output non-chimeric sequences to file
`uchimeout`	Output to chimera info to tab-separated file

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (x) 
{
  }