1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
|
## see list of possible command line options at the end.
## just for checking validity of arguments passed to eE from getExpression
.argCheck.eELegacy <- function(probFile, outFile, parFile=NULL, outputType=NULL, gibbs=NULL, trInfoFile=NULL, thetaActFile=NULL, MCMC_burnIn=NULL, MCMC_samplesN=NULL, MCMC_samplesSave=NULL, MCMC_samplesNmax=NULL, MCMC_chainsN=NULL, MCMC_scaleReduction=NULL, MCMC_dirAlpha=NULL, seed=NULL, verbose=NULL, pretend=FALSE){
return(TRUE);
}
.argCheck.eE <- function(probFile, outFile, parFile=NULL, outputType=NULL, gibbs=NULL, trInfoFile=NULL, thetaActFile=NULL, MCMC_burnIn=NULL, MCMC_samplesN=NULL, MCMC_samplesSave=NULL, MCMC_chainsN=NULL, MCMC_dirAlpha=NULL, seed=NULL, verbose=NULL, procN=NULL, pretend=FALSE){
return(TRUE);
}
## Call of estimateExpression which uses [new] default method for convergence checking.
estimateExpression <- function(probFile, outFile, parFile=NULL, outputType=NULL, gibbs=NULL, trInfoFile=NULL, thetaActFile=NULL, MCMC_burnIn=NULL, MCMC_samplesN=NULL, MCMC_samplesSave=NULL, MCMC_chainsN=NULL, MCMC_dirAlpha=NULL, seed=NULL, verbose=NULL, procN=NULL, pretend=FALSE){
args <- c('estimateExpression ',probFile, '--outPrefix', outFile)
if (!is.null(parFile)){
args <- c(args, '--parFile', parFile )
}
if (!is.null(outputType)) {
args <- c(args, '--outType', outputType)
}
if ((!is.null(gibbs)) && (gibbs)){
args <- c(args, '--gibbs')
}
if (!is.null(trInfoFile)) {
args <- c(args, '--trInfoFile', trInfoFile )
}
if (!is.null(thetaActFile)) {
args <- c(args, '--thetaActFile', thetaActFile)
}
if (!is.null( MCMC_burnIn)) {
args <- c(args, '--MCMC_burnIn',MCMC_burnIn )
}
if (!is.null( MCMC_samplesN)) {
args <- c(args, '--MCMC_samplesN', MCMC_samplesN)
}
if (!is.null( MCMC_samplesSave)) {
args <- c(args, '--MCMC_samplesSave',MCMC_samplesSave )
}
if (!is.null( MCMC_chainsN)) {
args <- c(args, '--MCMC_chainsN', MCMC_chainsN)
}
if (!is.null( MCMC_dirAlpha)) {
args <- c(args, '--MCMC_dirAlpha', MCMC_dirAlpha)
}
if (!is.null(seed)) {
args <- c(args, '--seed', seed)
}
if (!is.null(verbose) && (verbose)) {
args <- c(args, '--verbose')
}
if (!is.null(procN)) {
args <- c(args, '--procN', procN)
}
## print(args)
if(pretend){
writeLines(.specialPaste(args))
}else{
argc <- length(args);
## dyn.load(paste("src/estimateExpression", .Platform$dynlib.ext, sep=""));
result <- .C('_estimateExpression', as.integer(argc), as.character(args));
}
}
## Legacy call of estimateExpression which uses old method for convergence checking based on "--scaleReduction".
estimateExpressionLegacy <- function(probFile, outFile, parFile=NULL, outputType=NULL, gibbs=NULL, trInfoFile=NULL, thetaActFile=NULL, MCMC_burnIn=NULL, MCMC_samplesN=NULL, MCMC_samplesSave=NULL, MCMC_samplesNmax=NULL, MCMC_chainsN=NULL, MCMC_scaleReduction=NULL, MCMC_dirAlpha=NULL, seed=NULL, verbose=NULL, pretend=FALSE){
## , procN=NULL
args <- c('estimateExpression', '--scaleReduction',probFile, '--outPrefix', outFile)
if (!is.null(parFile)){
args <- c(args, '--parFile', parFile )
}
if (!is.null(outputType)) {
args <- c(args, '--outType', outputType)
}
if ((!is.null(gibbs)) && (gibbs)){
args <- c(args, '--gibbs')
}
if (!is.null(trInfoFile)) {
args <- c(args, '--trInfoFile', trInfoFile )
}
##if (!is.null(procN)) {
## args <- c(args, '--procN', procN)
##}
if (!is.null(thetaActFile)) {
args <- c(args, '--thetaActFile', thetaActFile)
}
if (!is.null( MCMC_burnIn)) {
args <- c(args, '--MCMC_burnIn',MCMC_burnIn )
}
if (!is.null( MCMC_samplesN)) {
args <- c(args, '--MCMC_samplesN', MCMC_samplesN)
}
if (!is.null( MCMC_samplesSave)) {
args <- c(args, '--MCMC_samplesSave',MCMC_samplesSave )
}
if (!is.null( MCMC_samplesNmax)) {
args <- c(args, '--MCMC_samplesNmax', MCMC_samplesNmax)
}
if (!is.null( MCMC_chainsN)) {
args <- c(args, '--MCMC_chainsN', MCMC_chainsN)
}
if (!is.null( MCMC_scaleReduction)) {
args <- c(args, '--MCMC_scaleReduction', MCMC_scaleReduction)
}
if (!is.null( MCMC_dirAlpha)) {
args <- c(args, '--MCMC_dirAlpha', MCMC_dirAlpha)
}
if (!is.null(seed)) {
args <- c(args, '--seed', seed)
}
if (!is.null(verbose) && (verbose)) {
args <- c(args, '--verbose')
}
## print(args)
if(pretend){
writeLines(.specialPaste(args))
}else{
argc <- length(args);
## dyn.load(paste("src/estimateExpression", .Platform$dynlib.ext, sep=""));
result <- .C('_estimateExpression', as.integer(argc), as.character(args));
}
}
## Options:
## --help
## Show this help information.
##
## --MCMC_burnIn=<MCMC_burnIn>
## Length of sampler's burn in period. (default: 1000)
##
## --MCMC_chainsN=<MCMC_chainsN>
## Number of parallel chains used. At least two chains will be used. (default: 4)
##
## --MCMC_dirAlpha=<MCMC_dirAlpha>
## Alpha parameter for the Dirichlet distribution. (default: 1)
##
## --MCMC_samplesDOmax
## Produce maximum number of samples (samplesNmax) in second iteration and quit. (default: Off)
##
## --MCMC_samplesN=<MCMC_samplesN>
## Initial number of samples produced. Doubles after every iteration. (default: 1000)
##
## --MCMC_samplesNmax=<MCMC_samplesNmax>
## Maximum number of samples produced in one iteration. After producing samplesNmax samples sampler finishes. (default: 50000)
##
## --MCMC_samplesSave=<MCMC_samplesSave>
## Number of samples recorder in total. (default: 1000)
##
## --MCMC_scaleReduction=<MCMC_scaleReduction>
## Target scale reduction, sampler finishes after this value is met. (default: 1.2)
##
## -G , --gibbs
## Use gibbs sampling instead of collapsed gibbs sampling. (default: Off)
##
## -o <outFilePrefix> , --outPrefix=<outFilePrefix>
## Prefix for the output files.
##
## -O <outputType> , --outType=<outputType>
## Output type (theta, RPKM, counts, tau). (default: theta)
##
## -p <parFileName> , --parFile=<parFileName>
## File containing parameters for the sampler, which can be otherwise specified by --MCMC* options. As the file is checked after every MCMC iteration, the parameters can be adjusted while running.
##
## -P <procN> , --procN=<procN>
## Limit the maximum number of threads to be used. (Default is the number of MCMC chains.)
##
## --scaleReduction
## Use scale reduction as stopping criterion, instead of computing effective sample size. (default: Off)
##
## -s <seed> , --seed=<seed>
## Random initialization seed.
##
## --thetaActFile=<thetaActFileName>
## File for logging noise parameter theta^{act}.
##
## -t <trInfoFileName> , --trInfoFile=<trInfoFileName>
## File containing transcript information. (Necessary for RPKM)
##
## -v , --verbose
## Verbose output. (default: Off)
|
