tests/README.md

In llrs/GSEAdv: Analyze Gene Sets Collections Properites

Tests and Coverage

25 noviembre, 2018 16:26:28

• Coverage
• Unit Tests

This output is created by covrpage.

Coverage

Coverage summary is created using the covr package.

| Object | Coverage (%) | |:---------------------------------------------------------------------|:------------:| | GSEAdv | 79.27 | | R/expand.R | 0.00 | | R/summary.R | 0.00 | | R/pathwaysPerGene.R | 14.29 | | R/calc-nPathways.R | 20.00 | | R/simulateGSC.R | 39.26 | | R/check-GSC.R | 71.43 | | R/estimate.R | 73.08 | | R/simulate2GSC.R | 78.38 | | R/fromSizeGenes_sizePathways.R | 78.57 | | R/as_GeneSetCollection.R | 83.33 | | R/sizesPer.R | 86.11 | | R/keep.R | 88.00 | | R/AllGenerics.R | 89.09 | | R/genesPerGene.R | 90.32 | | R/cond.R | 90.91 | | R/fromSizePathways.R | 92.50 | | R/pathway.R | 94.64 | | R/remove.R | 95.35 | | R/add.R | 96.30 | | R/nested.R | 97.14 | | R/adjacency.R | 100.00 | | R/completness.R | 100.00 | | R/distr.R | 100.00 | | R/duplicated.R | 100.00 | | R/edges.R | 100.00 | | R/estimate_sizes.R | 100.00 | | R/fromSizeGenes.R | 100.00 | | R/gene.R | 100.00 | | R/genesPerPathway.R | 100.00 | | R/modify.R | 100.00 | | R/n_functions.R | 100.00 | | R/sizes.R | 100.00 | | R/utilities.R | 100.00 | | R/zzz.R | 100.00 |

Unit Tests

Unit Test summary is created using the testthat package.

| file | n| time| error| failed| skipped| warning| |:----------------------------------------------------------------------------------|----:|------:|------:|-------:|--------:|--------:| | test_add.R | 11| 0.093| 0| 0| 0| 0| | test_asGeneSetCollection.R | 8| 0.040| 0| 0| 0| 0| | test_calcnPathways.R | 1| 0.003| 0| 0| 0| 0| | test_check.R | 1| 0.003| 0| 0| 0| 0| | test_completness.R | 1| 0.001| 0| 0| 0| 0| | test_condPer.R | 16| 0.042| 0| 0| 0| 0| | test_drop.R | 21| 0.111| 0| 0| 0| 0| | test_duplicates.R | 6| 0.010| 0| 0| 0| 0| | test_estimate_sizes.R | 2| 0.004| 0| 0| 0| 0| | test_fromSizeGenes_sizePathways.R | 3| 0.014| 0| 0| 0| 0| | test_fromSizeGenes.R | 2| 0.042| 0| 0| 0| 0| | test_fromSizePathways.R | 2| 0.015| 0| 0| 0| 0| | test_gene.R | 7| 0.039| 0| 0| 0| 0| | test_genesPerGene.R | 6| 0.027| 0| 0| 0| 0| | test_genesPerPathway.R | 5| 0.008| 0| 0| 0| 0| | test_keep.R | 2| 0.003| 0| 0| 0| 0| | test_keeps.R | 2| 0.015| 0| 0| 0| 0| | test_modify.R | 12| 0.062| 0| 0| 0| 0| | test_nested.R | 8| 0.066| 0| 0| 0| 0| | test_pathway.R | 7| 0.033| 0| 0| 0| 0| | test_simulations.R | 13| 0.266| 0| 0| 0| 0| | test_sizes.R | 22| 0.054| 0| 0| 0| 0| | test_sizesPer.R | 6| 0.015| 0| 0| 0| 0| | test_summary.R | 1| 0.003| 0| 0| 0| 0| | test_utilities.R | 21| 0.034| 0| 0| 0| 0| | test-adjacency.R | 2| 0.003| 0| 0| 0| 0| | test-distr.R | 4| 0.007| 0| 0| 0| 0| | test-edges.R | 3| 0.004| 0| 0| 0| 0| | test-estimate.R | 5| 0.006| 0| 0| 0| 0|

Show Detailed Test Results

| file | context | test | status | n| time| |:-------------------------------------------------------------------------------------|:-------------------------------------------------|:-----------------------------------|:-------|----:|------:| | test_add.R | Testing adding method | gene as character | PASS | 4| 0.049| | test_add.R | Testing adding method | pathway as character | PASS | 5| 0.027| | test_add.R | Testing adding method | pathway as character | PASS | 2| 0.017| | test_asGeneSetCollection.R | Testing list to GeneSetCollection method | info | PASS | 5| 0.029| | test_asGeneSetCollection.R | Testing list to GeneSetCollection method | as.GeneSetCollection | PASS | 3| 0.011| | test_calcnPathways.R | calc.nPathways | works | PASS | 1| 0.003| | test_check.R | Testing check-GSC methods | isolation | PASS | 1| 0.003| | test_completness.R | Testing utilities method | completness | PASS | 1| 0.001| | test_condPer.R | Testing cond* method | condPerGenes missing | PASS | 4| 0.009| | test_condPer.R | Testing cond* method | condPerGenes specific | PASS | 4| 0.020| | test_condPer.R | Testing cond* method | condPerPathways missing | PASS | 4| 0.006| | test_condPer.R | Testing cond* method | condPerPathways specific | PASS | 4| 0.007| | test_drop.R | Testing drop method | gene as character | PASS | 6| 0.025| | test_drop.R | Testing drop method | drop gene as numeric | PASS | 3| 0.014| | test_drop.R | Testing drop method | pathway as character | PASS | 2| 0.033| | test_drop.R | Testing drop method | drop pathway as numeric | PASS | 1| 0.009| | test_drop.R | Testing drop method | pathway as character | PASS | 3| 0.012| | test_drop.R | Testing drop method | pathway as character | PASS | 3| 0.010| | test_drop.R | Testing drop method | dropRel | PASS | 3| 0.008| | test_duplicates.R | Testing duplications | duplicatedPathways | PASS | 3| 0.005| | test_duplicates.R | Testing duplications | duplicatedGenes | PASS | 3| 0.005| | test_estimate_sizes.R | estimate.n* | estimate.nPathways works | PASS | 1| 0.002| | test_estimate_sizes.R | estimate.n* | estimate.nGenes works | PASS | 1| 0.002| | test_fromSizeGenes_sizePathways.R | Testing fromSizeGenes_sizePathways | fromSizeGenes_sizePathways | PASS | 3| 0.014| | test_fromSizeGenes.R | Testing fromSizeGenes method | fromSizeGenes | PASS | 2| 0.042| | test_fromSizePathways.R | Testing fromSizePathways method | fromSizePathways | PASS | 2| 0.015| | test_gene.R | Testing gene method | gene | PASS | 3| 0.007| | test_gene.R | Testing gene method | pathway | PASS | 4| 0.032| | test_genesPerGene.R | Testing genePerGene | gene as character | PASS | 2| 0.005| | test_genesPerGene.R | Testing genePerGene | gene as character | PASS | 2| 0.018| | test_genesPerGene.R | Testing genePerGene | gene as character | PASS | 2| 0.004| | test_genesPerPathway.R | genesPerPathway | default | PASS | 1| 0.002| | test_genesPerPathway.R | genesPerPathway | some pathway | PASS | 4| 0.006| | test_keep.R | Estimating numbers | double.factorial works | PASS | 2| 0.003| | test_keeps.R | keep.R | keepPPG works | PASS | 1| 0.003| | test_keeps.R | keep.R | keepGPP works | PASS | 1| 0.012| | test_modify.R | Testing modify method | gene as character | PASS | 6| 0.021| | test_modify.R | Testing modify method | pathway as character | PASS | 4| 0.026| | test_modify.R | Testing modify method | pathway as character | PASS | 2| 0.015| | test_nested.R | Testing nested method | nested | PASS | 2| 0.003| | test_nested.R | Testing nested method | compare | PASS | 6| 0.063| | test_pathway.R | Testing pathway method | pathway | PASS | 3| 0.007| | test_pathway.R | Testing pathway method | pathway | PASS | 4| 0.026| | test_simulations.R | Testing simulations to create GeneSetCollections | fromGPP_nGenes | PASS | 4| 0.035| | test_simulations.R | Testing simulations to create GeneSetCollections | fromPPG_nPathways | PASS | 5| 0.128| | test_simulations.R | Testing simulations to create GeneSetCollections | fromPPG_GPP | PASS | 4| 0.103| | test_sizes.R | Testing sizePathways and sizeGenes | Genes per Pathway and sizePathways | PASS | 3| 0.006| | test_sizes.R | Testing sizePathways and sizeGenes | Pathway per Genes and sizeGenes | PASS | 5| 0.010| | test_sizes.R | Testing sizePathways and sizeGenes | Pathway per Genes and sizeGenes | PASS | 3| 0.006| | test_sizes.R | Testing sizePathways and sizeGenes | Pathway per Genes and sizeGenes | PASS | 5| 0.018| | test_sizes.R | Testing sizePathways and sizeGenes | Same output sizeGenes | PASS | 3| 0.007| | test_sizes.R | Testing sizePathways and sizeGenes | Same output sizePathways | PASS | 3| 0.007| | test_sizesPer.R | | sizePathways | PASS | 2| 0.004| | test_sizesPer.R | | sizeGenes | PASS | 2| 0.004| | test_sizesPer.R | | sizePathways equivalent | PASS | 1| 0.004| | test_sizesPer.R | | sizePathways equivalent | PASS | 1| 0.003| | test_summary.R | Testing summary method | summary | PASS | 1| 0.003| | test_utilities.R | Testing utilities method | collectionType | PASS | 2| 0.002| | test_utilities.R | Testing utilities method | genesPerPathway | PASS | 3| 0.011| | test_utilities.R | Testing utilities method | pathwaysPerGene | PASS | 2| 0.003| | test_utilities.R | Testing utilities method | geneIdType | PASS | 2| 0.003| | test_utilities.R | Testing utilities method | nGenes | PASS | 1| 0.001| | test_utilities.R | Testing utilities method | nPathways | PASS | 1| 0.001| | test_utilities.R | Testing utilities method | h_index | PASS | 4| 0.005| | test_utilities.R | Testing utilities method | IC | PASS | 4| 0.006| | test_utilities.R | Testing utilities method | inverseList | PASS | 1| 0.001| | test_utilities.R | Testing utilities method | names_vec | PASS | 1| 0.001| | test-adjacency.R | test-adjacency | adjacency works | PASS | 2| 0.003| | test-distr.R | test-distr | distrGenes works | PASS | 2| 0.004| | test-distr.R | test-distr | distrPathways works | PASS | 2| 0.003| | test-edges.R | test-edges | edges works | PASS | 1| 0.002| | test-edges.R | test-edges | nEdges works | PASS | 1| 0.001| | test-edges.R | test-edges | edges and nEdges match | PASS | 1| 0.001| | test-estimate.R | test-estimate | estimate works | PASS | 5| 0.006|

Session Info

| Field | Value | |:---------|:------------------------------| | Version | R version 3.5.1 (2018-07-02) | | Platform | x86_64-pc-linux-gnu (64-bit) | | Running | Ubuntu 18.04.1 LTS | | Language | en_US | | Timezone | Europe/Madrid |

| Package | Version | |:---------|:--------| | testthat | 2.0.1 | | covr | 3.2.1 | | covrpage | 0.0.65 |

llrs/GSEAdv documentation built on May 29, 2019, 6 p.m.