Populates and returns output files for a given protocol

Returns the pipeline outputs which are defined in the pipeline interface indicated in the Project-class

outputsByProtocols(project, ...)

# S4 method for Project
outputsByProtocols(project, protocolNames = NULL)

Arguments

project	Project-class object
...	other arguments passed to methods
protocolNames	char vector of protocol names to match the pipelines and return their outputs

Value

a list of output file paths. The order of the first level of the list corresponds to the order of the pipeline interface files, second level order (named) reflects the pipelines within the files, the last level is a named list of file paths populated by the samples

Methods (by class)

• Project: extracts pipeline outputs for a given protocol or set of protocols

Examples

projectConfig = system.file("extdata",
"example_peps-master",
"example_piface",
"project_config.yaml",
package = "BiocProject")
p = Project(file = projectConfig)
#> Loaded config file: /Users/mstolarczyk/Uczelnia/UVA/code/BiocProject/inst/extdata/example_peps-master/example_piface/project_config.yaml
outputsByProtocols(p, "PROTO2")
#> [[1]]
#> [[1]]$PROTO2
#> [[1]]$PROTO2$pipeline2.py
#> [[1]]$PROTO2$pipeline2.py$output1
#> [[1]]$PROTO2$pipeline2.py$output1$sample3
#> [1] "/Users/mstolarczyk/Uczelnia/UVA/code/BiocProject/inst/extdata/example_peps-master/example_piface/../output/results_pipeline/sample3//pipeline2/sample3_GSM2471249_1.bw"
#> 
#> 
#> [[1]]$PROTO2$pipeline2.py$output2
#> [[1]]$PROTO2$pipeline2.py$output2$sample3
#> [1] "/Users/mstolarczyk/Uczelnia/UVA/code/BiocProject/inst/extdata/example_peps-master/example_piface/../output/results_pipeline/sample3//pipeline2/sample3_GSM2471249_2.bw"
#> 
#> 
#> 
#> 
#> 
#> [[2]]
#> [[2]]$PROTO2
#> [[2]]$PROTO2$other_pipeline2.py
#> [[2]]$PROTO2$other_pipeline2.py$output1
#> [[2]]$PROTO2$other_pipeline2.py$output1$sample3
#> [1] "/Users/mstolarczyk/Uczelnia/UVA/code/BiocProject/inst/extdata/example_peps-master/example_piface/../output/results_pipeline/sample3//other_pipeline2/sample3_GSM2471249_1.bw"
#> 
#> 
#> [[2]]$PROTO2$other_pipeline2.py$output2
#> [[2]]$PROTO2$other_pipeline2.py$output2$sample3
#> [1] "/Users/mstolarczyk/Uczelnia/UVA/code/BiocProject/inst/extdata/example_peps-master/example_piface/../output/results_pipeline/sample3//other_pipeline2/sample3_GSM2471249_2.bw"
#> 
#> 
#> 
#> 
#>