estimateVBExpression1
Estimate expression given precomputed probabilities of (observed) reads alignments
Usage
estimateVBExpression -o
<outFilePrefix>
[OPTIONS]
[prob
file]
Overview
Estimates expression given precomputed probabilities of (observed) reads' alignments.
-
Uses Variational Bayes algorithm to produce parameters for distribution of relative abundances.
Options
--help
-
Show this help information.
--optLimit=<limit>
-
Optimisation limit in terms of minimal gradient or change of bound. (default: 1e-05)
--maxIter=<maxIter>
-
Maximum number of iterations. (default: 10000)
-m <optMethod> , --method=<optMethod>
-
Optimization method (steepest, PR, FR, HS). (default: FR)
-o <outFilePrefix> , --outPrefix=<outFilePrefix>
-
Prefix for the output files.
-O <outputType> , --outType=<outputType>
-
Output type (theta, RPKM, counts) of the samples sampled from the distribution. (default: theta)
-P <procN> , --procN=<procN>
-
Limit the maximum number of threads to be used. (default: 4)
--samples=<samples>
-
Number of samples to be sampled from the distribution.
-s <seed> , --seed=<seed>
-
Random initialization seed.
-t <trInfoFileName> , --trInfoFile=<trInfoFileName>
-
File containing transcript information. (Necessary for RPKM samples)
-v , --verbose
-
Verbose output. (default: Off)
-V , --veryVerbose
-
More verbose output, better if output forwarded into file. (default: Off)
History
- Debian 13 (Trixie) to Debian 12 (Bookworm): the text shown here
- Debian 11 (Bullseye)
- Debian 10 (Buster)