testMultireadFunctional: Functions dedicated to the functional validation of multiread...
In Pasha: Preprocessing of Aligned Sequences from HTS Analyses

Description Usage Arguments Details Value Author(s) See Also

The goal of these two functions is to generate a reference dataset with the currently installed Pasha package in the user's environment and/or to compare it to the precomputed results in the developpers environment.

.testFunctionalMultiread(folderOutput=tempdir(), 
                         testType="regular",
                         verbose=FALSE) 

.testFunctionalMultiread_generateResults(testFileBOW_folderName,
                                         testFileBOW_fileName,
                                         folderOutputGenerated, 
                                         verbosity=0)

`folderOutput`	An existing folder (this is tested and can eventually raise an error) in which the generated results will be written and the precomputed results will be inflated.
`testFileBOW_folderName`	The folder in which the .bow file for results generation stands (.testFunctionalMultiread passes the path to the package-embedded test .bow file)
`testFileBOW_fileName`	The filename of the ?bow file used to generate the results (.testFunctionalMultiread passes the name of the package-embedded test .bow file)
`folderOutputGenerated`	The folder in which the intermediary generated data files stands (.testFunctionalMultiread passes this path)
`testType`	A value in c("regular", "complete"). A regular test will generate multiread specific results but skips files for which comparison can be problematic because of writing floating points with C++ routines (which formatting depends on the machine/platform floating numbers implementation). Because this test function is called for package validation, a regular test exclude these files which would otherwise prevent the package validation. A complete test can still be done manually for testing purposes.
`verbose`	Logical. If verbose is FALSE, the test stdout will be redirected to a log file to avoid overflow of test messages.
`verbosity`	An integer. The verbose level : 0 = no message, 1 = trace level

Once installed, Pasha gives access to a functional test of features linked to multiread management with the function '.testFunctionalMultiread'.

The package includes a .bow file (obtained throufh bowtie with –concise option) designed to cover most of the cases for multiread datasets (see publication for details). This test consists in using the provided R funcntions and the embedded .bow file to generate results and compare them to a previously generated (precomputed) dataset that has been functionally validated by developpers. The precomputed dataset is embedded in the package in a zip file and contains all the .bow and .txt files that could be necessary for validation. This dataset is generated and compiled by package developpers using .testFunctionalMultiread_generateResults.

.testFunctionalMultiread prints to stdout a summary of file generation and comparison with reference dataset.

Lionel Spinelli

processPipeline

Pasha documentation built on Jan. 15, 2017, 6:21 p.m.