Description Usage Arguments Author(s)
Test the correlation coefficient beween a segment of coverage depth and a vector of 100 integers modeling a simple shape of sharp increases (or decreases) in transcription: x =[0..0,1..1] (or x =[1..1,0..0]).
1 2 3 4 | compile.confirmed.operons(genes.and.operons, transcCDSs, transcIGRs.pos,
transcIGRs.neg, POSSs, POESs, minExprCDS = 0.1, minExprIGR = 0.25,
max.start.transc = c(0.1, 0.1), max.end.transc = c(0.1, 0.1),
verbose = TRUE, ...)
|
genes.and.operons |
Data table merging gene(s) and operon(s) annotations. See |
transcCDSs |
Transcription levels for the coding regions. See |
transcIGRs.pos |
Transcription levels for the intergenic regions (forard strand). See |
transcIGRs.neg |
Transcription levels for the intergenic regions (reverse strand). See |
POSSs |
Data table representing a set of putative operon start-points. |
POESs |
Data table representing a set of putative operon end-points. |
minExprCDS |
Minimum expression level for the coding sequence regions (CDSs). Default values is 0.1. |
minExprIGR |
Minimum expression level for the intergenic regions (IGRs). Default values is 0.25. |
max.start.transc |
Cutoff values for the start transcription points. Default values is 0.1. |
max.end.transc |
Cutoff values for the end transcription points. Default values is 0.1. |
verbose |
Default logical value is TRUE. |
Vittorio Fortino compile.confirmed.operons()
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