| Type: | Package |
| Title: | Sampler for Verification Studies |
| Version: | 1.0.0 |
| Date: | 2018-02-05 |
| Author: | Chris Cooper [aut], Dorota H. Sendorek [ctb], Paul C. Boutros [cre, cph] |
| Maintainer: | Paul C. Boutros <Paul.Boutros@oicr.on.ca> |
| Description: | A binding for the 'valection' program which offers various ways to sample the outputs of competing algorithms or parameterizations, and fairly assess their performance against each other. The 'valection' C library is required to use this package and can be downloaded from: http://labs.oicr.on.ca/boutros-lab/software/valection. Cooper CI, et al; Valection: Design Optimization for Validation and Verification Studies; Biorxiv 2018; <doi:10.1101/254839>. |
| Depends: | R (≥ 3.1.0) |
| SystemRequirements: | valection (>= 1.0.0) |
| URL: | http://labs.oicr.on.ca/boutros-lab/software/valection |
| License: | GPL-3 |
| Imports: | testthat |
| RoxygenNote: | 6.0.1 |
| NeedsCompilation: | no |
| Packaged: | 2018-02-05 21:59:06 UTC; clalansingh |
| Repository: | CRAN |
| Date/Publication: | 2018-02-06 09:29:33 UTC |
Check for library
Description
Check if library is available
Usage
check.for.library(lib.name = 'valection');
Arguments
lib.name |
A string of the library name. Defaults to 'valection'. |
Details
Used internally to check if executable is available in PATH.
Value
A logical indicating presence of library
Author(s)
Dorota Sendorek
Handle missing library
Description
Output error message for missing library
Usage
handle.missing.library(lib.name = 'valection');
Arguments
lib.name |
A string of the library name. Defaults to 'valection'. |
Details
Used internally to output an error message for missing library.
Author(s)
Dorota Sendorek
Enquote a string
Description
Add single quotation marks around a string
Usage
quoted(string);
Arguments
string |
A string |
Details
Used internally to create bash commands.
Value
A string
Author(s)
Chris Cooper and Dorota Sendorek
Run the decreasing with overlap algorithm
Description
Runs the decreasing with overlap algorithm from the valection library.
Usage
run.decreasing.with.overlap(budget, infile, outfile, seed);
Arguments
budget |
An integer specifying the number of candidates to select. |
infile |
Path to input file. It should be formatted with a tab separating the caller and call on each line. caller1 name a call this caller made caller2 name a call this caller made |
outfile |
Path to a filename where the calls should be outputted. |
seed |
An integer specifying the random seed value. Optional. |
Details
Sampling calls where the likelihood of a call getting selected is inversely proportional to the number of callers that made the call.
Author(s)
Chris Cooper
Examples
## Not run:
run.decreasing.with.overlap(
budget = 5,
infile = system.file("extdata/infile_example.tsv", package = "valection"),
outfile = "outfile_decreasingWithOverlap.txt"
);
## End(Not run)Run the directed sampling algorithm
Description
Runs the directed sampling algorithm from the valection library.
Usage
run.directed.sampling(budget, infile, outfile, seed);
Arguments
budget |
An integer specifying the number of candidates to select. |
infile |
Path to input file. It should be formatted with a tab separating the caller and call on each line. caller1 name a call this caller made caller2 name a call this caller made |
outfile |
Path to a filename where the calls should be outputted. |
seed |
An integer specifying the random seed value. Optional. |
Details
Sampling calls where a) an equal number of calls is selected from each caller and b) the likelihood of a call getting selected is proportional to the number of callers that made it.
Author(s)
Chris Cooper
Examples
## Not run:
run.directed.sampling(
budget = 5,
infile = system.file("extdata/infile_example.tsv", package = "valection"),
outfile = "outfile_directedSampling.txt"
);
## End(Not run)Run the equal per caller algorithm
Description
Runs the equal per caller algorithm from the valection library.
Usage
run.equal.per.caller(budget, infile, outfile, seed);
Arguments
budget |
An integer specifying the number of candidates to select. |
infile |
Path to input file. It should be formatted with a tab separating the caller and call on each line. caller1 name a call this caller made caller2 name a call this caller made |
outfile |
Path to a filename where the calls should be outputted. |
seed |
An integer specifying the random seed value. Optional. |
Details
Sampling calls where an equal number of calls is selected from each caller.
Author(s)
Chris Cooper
Examples
## Not run:
run.equal.per.caller(
budget = 5,
infile = system.file("extdata/infile_example.tsv", package = "valection"),
outfile = "outfile_runEqualPerCaller.txt"
);
## End(Not run)Run the equal per overlap algorithm
Description
Runs the equal per overlap algorithm from the valection library.
Usage
run.equal.per.overlap(budget, infile, outfile, seed);
Arguments
budget |
An integer specifying the number of candidates to select. |
infile |
Path to input file. It should be formatted with a tab separating the caller and call on each line. caller1 name a call this caller made caller2 name a call this caller made |
outfile |
Path to a filename where the calls should be outputted. |
seed |
An integer specifying the random seed value. Optional. |
Details
Sampling calls by, first, grouping calls by number of callers making the call and, second, selecting an equal number of calls from each group.
Author(s)
Chris Cooper
Examples
## Not run:
run.equal.per.overlap(
budget = 5,
infile = system.file("extdata/infile_example.tsv", package = "valection"),
outfile = "outfile_equalPerOverlap.txt"
);
## End(Not run)Run the increasing with overlap algorithm
Description
Runs the increasing with overlap algorithm from the valection library.
Usage
run.increasing.with.overlap(budget, infile, outfile, seed);
Arguments
budget |
An integer specifying the number of candidates to select. |
infile |
Path to input file. It should be formatted with a tab separating the caller and call on each line. caller1 name a call this caller made caller2 name a call this caller made |
outfile |
Path to a filename where the calls should be outputted. |
seed |
An integer specifying the random seed value. Optional. |
Details
Sampling calls where the likelihood of a call getting selected is proportional to the number of callers that made the call.
Author(s)
Chris Cooper
Examples
## Not run:
run.increasing.with.overlap(
budget = 5,
infile = system.file("extdata/infile_example.tsv", package = "valection"),
outfile = "outfile_increasingWithOverlap.txt"
);
## End(Not run)Run the random sampling algorithm
Description
Runs the random sampling algorithm from the valection library.
Usage
run.random.sampling(budget, infile, outfile, seed);
Arguments
budget |
An integer specifying the number of candidates to select. |
infile |
Path to input file. It should be formatted with a tab separating the caller and call on each line. caller1 name a call this caller made caller2 name a call this caller made |
outfile |
Path to a filename where the calls should be outputted. |
seed |
An integer specifying the random seed value. Optional. |
Details
Sampling calls randomly where each call has an equal probability of getting selected.
Author(s)
Chris Cooper
Examples
## Not run:
run.random.sampling(
budget = 5,
infile = system.file("extdata/infile_example.tsv", package = "valection"),
outfile = "outfile_randomSampling.txt"
);
## End(Not run)