[med-svn] [bitseq] 06/14: Add more manpages

[Andreas Tille]

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tille pushed a commit to branch master
in repository bitseq.

commit d1e487b858db4107cdbcb31f6f4f39e6f8c8fb04
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jan 1 19:15:07 2014 +0000

    Add more manpages
---
 debian/mans/convertSamples.1     | 43 ++++++++++++++++++++
 debian/mans/estimateDE.1         | 50 +++++++++++++++++++++++
 debian/mans/estimateExpression.1 | 87 ++++++++++++++++++++++++++++++++++++++++
 3 files changed, 180 insertions(+)

diff --git a/debian/mans/convertSamples.1 b/debian/mans/convertSamples.1
new file mode 100644
index 0000000..3e5c010
--- /dev/null
+++ b/debian/mans/convertSamples.1
@@ -0,0 +1,43 @@
+.TH CONVERTSAMPLES "1" "January 2014" "convertSamples 0.7.0" "User Commands"
+.SH NAME
+convertSamples \- convert or normalize MCMC expression samples
+.SH SYNOPSIS
+.B convertSamples
+\fI-a <action> -o <outFileName>  \fR[\fIOPTIONS\fR] [\fIsampleFile\fR]
+.SH DESCRIPTION
+Converts or normalizes MCMC expression samples.
+.IP
+[sampleFile] should contain transposed MCMC samples.
+.SH OPTIONS
+.HP
+\fB\-\-help\fR
+.IP
+Show this help information.
+.HP
+\fB\-\-Nmap=\fR<Nmap>
+.IP
+Total number of aligned reads. Or a normalization constant, when normalizing.
+.HP
+\fB\-a\fR <action> ,   \fB\-\-action=\fR<action>
+.IP
+Action to perform options:
+.IP
+T2R \- theta to rpkm
+R2T \- rpkm to theta
+T2RL \- theta to log\-rpkm
+C2R \- counts to rpkm
+R2C \- rpkm 2 counts
+NORM \- normalize (samples are multiplied by Nmap)
+LOGNORM \- log+normalize (samples are multiplied by Nmap and logged).
+.HP
+\fB\-o\fR <outFileName> ,   \fB\-\-outFile=\fR<outFileName>
+.IP
+Name of the output file.
+.HP
+\fB\-t\fR <trInfoFileName> ,   \fB\-\-trInfoFile=\fR<trInfoFileName>
+.IP
+File containing transcript information.
+.HP
+\fB\-v\fR ,   \fB\-\-verbose\fR
+.IP
+Verbose output. (default: Off)
diff --git a/debian/mans/estimateDE.1 b/debian/mans/estimateDE.1
new file mode 100644
index 0000000..ff82155
--- /dev/null
+++ b/debian/mans/estimateDE.1
@@ -0,0 +1,50 @@
+.TH ESTIMATEDE "1" "January 2014" "estimateDE 0.7.0" "User Commands"
+.SH NAME
+estimateDE \- this bitseq module estimates differential expression from data sets
+.SH SYNOPSIS
+.B estimateDE
+\fI\-o <outFilePrefix> \-p <parFileName>  \fR[\fIOPTIONS\fR] [\fIsampleFiles\fR]
+.SH DESCRIPTION
+Estimate differential expression from the dataset.
+.IP
+[sampleFiles] should contain transposed MCMC samples from replicates.
+To distinguish conditions use C between them e.g.:
+.IP
+samplesC1\-R1.rpkm samplesC1\-R2.rpkm C samplesC2\-R1.rpkm samplesC2\-R2.rpkm
+.SH OPTIONS
+.HP
+\fB\-\-help\fR
+.IP
+Show this help information.
+.HP
+\fB\-\-confidenceInterval=\fR<cf>
+.IP
+Percentage for confidence intervals. (default: 95)
+.HP
+\fB\-l\fR <lambda0> ,   \fB\-\-lambda0=\fR<lambda0>
+.IP
+Parameter lambda_0. (default: 2)
+.HP
+\fB\-\-norm=\fR<normalization>
+.IP
+Normalization constants for each input file provided as comma separated list of doubles (e.g. 1.0017,1.0,0.9999 ).
+.HP
+\fB\-o\fR <outFilePrefix> ,   \fB\-\-outPrefix=\fR<outFilePrefix>
+.IP
+Prefix for the output files.
+.HP
+\fB\-p\fR <parFileName> ,   \fB\-\-parameters=\fR<parFileName>
+.IP
+File containing estimated hyperparameters.
+.HP
+\fB\-s\fR ,   \fB\-\-samples\fR
+.IP
+Produce samples of condition mean expression apart from PPLR and confidence. (default: Off)
+.HP
+\fB\-\-seed=\fR<seed>
+.IP
+Random initialization seed.
+.HP
+\fB\-v\fR ,   \fB\-\-verbose\fR
+.IP
+Verbose output. (default: Off)
diff --git a/debian/mans/estimateExpression.1 b/debian/mans/estimateExpression.1
new file mode 100644
index 0000000..30f8634
--- /dev/null
+++ b/debian/mans/estimateExpression.1
@@ -0,0 +1,87 @@
+.TH ESTIMATEEXPRESSION "1" "January 2014" "estimateExpression 0.7.0" "User Commands"
+.SH NAME
+estimateExpression \- estimate expression given precomputed probabilities of (observed) reads' alignments
+.SH SYNOPSIS
+.B estimateExpression
+\fI-o <outFilePrefix>  \fR[\fIOPTIONS\fR] [\fIprob file\fR]
+.SH DESCRIPTION
+Estimates expression given precomputed probabilities of (observed) reads' alignments.
+.IP
+Uses MCMC sampling algorithm to produce relative abundance or RPKM.
+.SH OPTIONS
+.HP
+\fB\-\-help\fR
+.IP
+Show this help information.
+.HP
+\fB\-\-MCMC_burnIn=\fR<MCMC_burnIn>
+.IP
+Length of sampler's burn in period. (default: 1000)
+.HP
+\fB\-\-MCMC_chainsN=\fR<MCMC_chainsN>
+.IP
+Number of parallel chains used. At least two chains will be used. (default: 4)
+.HP
+\fB\-\-MCMC_dirAlpha=\fR<MCMC_dirAlpha>
+.IP
+Alpha parameter for the Dirichlet distribution. (default: 1)
+.HP
+\fB\-\-MCMC_samplesDOmax\fR
+.IP
+Produce maximum number of samples (samplesNmax) in second iteration and quit. (default: Off)
+.HP
+\fB\-\-MCMC_samplesN=\fR<MCMC_samplesN>
+.IP
+Initial number of samples produced. Doubles after every iteration. (default: 1000)
+.HP
+\fB\-\-MCMC_samplesNmax=\fR<MCMC_samplesNmax>
+.IP
+Maximum number of samples produced in one iteration. After producing samplesNmax samples sampler finishes. (default: 50000)
+.HP
+\fB\-\-MCMC_samplesSave=\fR<MCMC_samplesSave>
+.IP
+Number of samples recorder in total. (default: 1000)
+.HP
+\fB\-\-MCMC_scaleReduction=\fR<MCMC_scaleReduction>
+.IP
+Target scale reduction, sampler finishes after this value is met. (default: 1.2)
+.HP
+\fB\-G\fR ,   \fB\-\-gibbs\fR
+.IP
+Use Gibbs sampling instead of collapsed Gibbs sampling. (default: Off)
+.HP
+\fB\-o\fR <outFilePrefix> ,   \fB\-\-outPrefix=\fR<outFilePrefix>
+.IP
+Prefix for the output files.
+.HP
+\fB\-O\fR <outputType> ,   \fB\-\-outType=\fR<outputType>
+.IP
+Output type (theta, RPKM, counts, tau). (default: theta)
+.HP
+\fB\-p\fR <parFileName> ,   \fB\-\-parFile=\fR<parFileName>
+.IP
+File containing parameters for the sampler, which can be otherwise specified by \fB\-\-MCMC\fR* options. As the file is checked after every MCMC iteration, the parameters can be adjusted while running.
+.HP
+\fB\-P\fR <procN> ,   \fB\-\-procN=\fR<procN>
+.IP
+Limit the maximum number of threads to be used. (Default is the number of MCMC chains.)
+.HP
+\fB\-\-scaleReduction\fR
+.IP
+Use scale reduction as stopping criterion, instead of computing effective sample size. (default: Off)
+.HP
+\fB\-s\fR <seed> ,   \fB\-\-seed=\fR<seed>
+.IP
+Random initialization seed.
+.HP
+\fB\-\-thetaActFile=\fR<thetaActFileName>
+.IP
+File for logging noise parameter theta^{act}.
+.HP
+\fB\-t\fR <trInfoFileName> ,   \fB\-\-trInfoFile=\fR<trInfoFileName>
+.IP
+File containing transcript information. (Necessary for RPKM)
+.HP
+\fB\-v\fR ,   \fB\-\-verbose\fR
+.IP
+Verbose output. (default: Off)

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