context("Test creating gene label data that RCircos will accept from a list of Fusion object")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
context("Test creating link data that RCircos will accept from a list of Fusion object")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"No protein domains are retained in the downstream gene, because the fusion is not in frame. But since plotDownstreamProteinDomainsIfFusionIsOutOfFrame = TRUE, we'll plot the protein domains in the downstream gene anyway..")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
testthat::test_that("selectTranscript gives exonBoundary transcripts when we ask for withinExon transcripts, because there are no witinExon transcripts", {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
testthat::expect_message(selectTranscript(fusion@geneA, "withinExon"), "..found transcripts of type exonBoundary")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
testthat::test_that("selectTranscript gives error with whichTranscripts=\"4242\" when there are no such transcripts", {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
testthat::test_that("selectTranscript returns the expected specific transcripts", {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
test_that("getEnsemblIds gets the correct Ensembl gene ids for a fusion object", {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tests/testthat/test_createFusionReport.R:7:10: style: Put spaces around all infix operators.
tests/testthat/test_createFusionReport.R:10:1: style: Variable and function names should be all lowercase.
tests/testthat/test_createFusionReport.R:16:31: style: Variable and function names should be all lowercase.
tests/testthat/test_createFusionReport.R:18:26: style: Variable and function names should be all lowercase.
tests/testthat/test_fusionsToGeneLabelData.R:1:1: style: lines should not be more than 80 characters.
tests/testthat/test_fusionsToGeneLabelData.R:6:10: style: Put spaces around all infix operators.
tests/testthat/test_fusionsToGeneLabelData.R:8:1: style: Variable and function names should be all lowercase.
tests/testthat/test_fusionsToGeneLabelData.R:8:14: style: Variable and function names should be all lowercase.
tests/testthat/test_fusionsToGeneLabelData.R:11:23: style: Variable and function names should be all lowercase.
tests/testthat/test_fusionsToGeneLabelData.R:12:1: style: lines should not be more than 80 characters.
tests/testthat/test_fusionsToGeneLabelData.R:12:29: style: Variable and function names should be all lowercase.
tests/testthat/test_fusionsToLinkData.R:1:1: style: lines should not be more than 80 characters.
tests/testthat/test_fusionsToLinkData.R:6:10: style: Put spaces around all infix operators.
tests/testthat/test_fusionsToLinkData.R:8:1: style: Variable and function names should be all lowercase.
tests/testthat/test_fusionsToLinkData.R:8:13: style: Variable and function names should be all lowercase.
tests/testthat/test_fusionsToLinkData.R:11:23: style: Variable and function names should be all lowercase.
tests/testthat/test_fusionsToLinkData.R:12:1: style: lines should not be more than 80 characters.
tests/testthat/test_fusionsToLinkData.R:12:29: style: Variable and function names should be all lowercase.
tests/testthat/test_getFusionBy.R:6:10: style: Put spaces around all infix operators.
tests/testthat/test_importDefuse.R:5:35: style: Put spaces around all infix operators.
tests/testthat/test_importEricscript.R:3:1: style: Variable and function names should be all lowercase.
tests/testthat/test_importEricscript.R:7:29: style: Variable and function names should be all lowercase.
tests/testthat/test_importEricscript.R:19:33: style: Variable and function names should be all lowercase.
tests/testthat/test_importEricscript.R:20:33: style: Variable and function names should be all lowercase.
tests/testthat/test_importEricscript.R:24:40: style: Variable and function names should be all lowercase.
tests/testthat/test_importFusionmap.R:3:1: style: Variable and function names should be all lowercase.
tests/testthat/test_importFusionmap.R:7:28: style: Variable and function names should be all lowercase.
tests/testthat/test_importFusionmap.R:19:32: style: Variable and function names should be all lowercase.
tests/testthat/test_importFusionmap.R:20:32: style: Variable and function names should be all lowercase.
tests/testthat/test_importFusionmap.R:24:39: style: Variable and function names should be all lowercase.
tests/testthat/test_importInfusion.R:3:1: style: Variable and function names should be all lowercase.
tests/testthat/test_importInfusion.R:7:27: style: Variable and function names should be all lowercase.
tests/testthat/test_importInfusion.R:19:31: style: Variable and function names should be all lowercase.
tests/testthat/test_importInfusion.R:20:31: style: Variable and function names should be all lowercase.
tests/testthat/test_importInfusion.R:24:38: style: Variable and function names should be all lowercase.
tests/testthat/test_importJaffa.R:3:1: style: Variable and function names should be all lowercase.
tests/testthat/test_importJaffa.R:7:24: style: Variable and function names should be all lowercase.
tests/testthat/test_importJaffa.R:20:28: style: Variable and function names should be all lowercase.
tests/testthat/test_importJaffa.R:21:28: style: Variable and function names should be all lowercase.
tests/testthat/test_importJaffa.R:25:35: style: Variable and function names should be all lowercase.
tests/testthat/test_importPrada.R:3:1: style: Variable and function names should be all lowercase.
tests/testthat/test_importPrada.R:7:24: style: Variable and function names should be all lowercase.
tests/testthat/test_importPrada.R:20:28: style: Variable and function names should be all lowercase.
tests/testthat/test_importPrada.R:21:28: style: Variable and function names should be all lowercase.
tests/testthat/test_importPrada.R:25:35: style: Variable and function names should be all lowercase.
tests/testthat/test_importStarfusion.R:3:1: style: Variable and function names should be all lowercase.
tests/testthat/test_importStarfusion.R:7:29: style: Variable and function names should be all lowercase.
tests/testthat/test_importStarfusion.R:20:33: style: Variable and function names should be all lowercase.
tests/testthat/test_importStarfusion.R:21:33: style: Variable and function names should be all lowercase.
tests/testthat/test_importStarfusion.R:25:40: style: Variable and function names should be all lowercase.
tests/testthat/test_lintr.R:7:1: style: Trailing blank lines are superfluous.
tests/testthat/test_plotCircle.R:7:10: style: Put spaces around all infix operators.
tests/testthat/test_plotCircle.R:10:1: style: Variable and function names should be all lowercase.
tests/testthat/test_plotCircle.R:17:7: style: Variable and function names should be all lowercase.
tests/testthat/test_plotCircle.R:23:26: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusion.R:7:10: style: Put spaces around all infix operators.
tests/testthat/test_plotFusion.R:11:1: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusion.R:14:10: style: Put spaces around all infix operators.
tests/testthat/test_plotFusion.R:15:25: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusion.R:20:12: style: Put spaces around all infix operators.
tests/testthat/test_plotFusion.R:24:3: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusion.R:29:7: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusion.R:40:26: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusion.R:47:3: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusion.R:52:7: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusion.R:62:26: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusion.R:71:3: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusion.R:73:23: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusion.R:75:3: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusion.R:77:23: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionReads.R:7:10: style: Put spaces around all infix operators.
tests/testthat/test_plotFusionReads.R:14:10: style: Put spaces around all infix operators.
tests/testthat/test_plotFusionReads.R:16:1: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionReads.R:24:40: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionReads.R:30:1: style: lines should not be more than 80 characters.
tests/testthat/test_plotFusionReads.R:30:3: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionReads.R:31:3: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionReads.R:31:41: style: Put spaces around all infix operators.
tests/testthat/test_plotFusionReads.R:33:7: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionReads.R:33:28: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionReads.R:33:49: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionReads.R:39:26: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionTranscript.R:7:10: style: Put spaces around all infix operators.
tests/testthat/test_plotFusionTranscript.R:11:1: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionTranscript.R:14:10: style: Put spaces around all infix operators.
tests/testthat/test_plotFusionTranscript.R:15:25: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionTranscript.R:17:1: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionTranscript.R:24:7: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionTranscript.R:34:26: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionTranscriptsGraph.R:7:10: style: Put spaces around all infix operators.
tests/testthat/test_plotFusionTranscriptsGraph.R:11:1: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionTranscriptsGraph.R:14:10: style: Put spaces around all infix operators.
tests/testthat/test_plotFusionTranscriptsGraph.R:15:25: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionTranscriptsGraph.R:17:1: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionTranscriptsGraph.R:24:7: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionTranscriptsGraph.R:34:26: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionTranscriptWithProteinDomain.R:7:10: style: Put spaces around all infix operators.
tests/testthat/test_plotFusionTranscriptWithProteinDomain.R:11:1: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionTranscriptWithProteinDomain.R:12:1: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionTranscriptWithProteinDomain.R:14:1: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionTranscriptWithProteinDomain.R:17:10: style: Put spaces around all infix operators.
tests/testthat/test_plotFusionTranscriptWithProteinDomain.R:18:25: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionTranscriptWithProteinDomain.R:23:10: style: Put spaces around all infix operators.
tests/testthat/test_plotFusionTranscriptWithProteinDomain.R:28:10: style: Put spaces around all infix operators.
tests/testthat/test_plotFusionTranscriptWithProteinDomain.R:30:1: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionTranscriptWithProteinDomain.R:37:7: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionTranscriptWithProteinDomain.R:45:25: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionTranscriptWithProteinDomain.R:46:25: style: Variable and function names should be all lowercase.
tests/testthat/test_plotFusionTranscriptWithProteinDomain.R:48:1: style: lines should not be more than 80 characters.
tests/testthat/test_plotFusionTranscriptWithProteinDomain.R:52:26: style: Variable and function names should be all lowercase.
tests/testthat/test_plotTranscripts.R:7:10: style: Put spaces around all infix operators.
tests/testthat/test_plotTranscripts.R:11:1: style: Variable and function names should be all lowercase.
tests/testthat/test_plotTranscripts.R:14:10: style: Put spaces around all infix operators.
tests/testthat/test_plotTranscripts.R:15:25: style: Variable and function names should be all lowercase.
tests/testthat/test_plotTranscripts.R:17:1: style: Variable and function names should be all lowercase.
tests/testthat/test_plotTranscripts.R:24:7: style: Variable and function names should be all lowercase.
tests/testthat/test_plotTranscripts.R:34:26: style: Variable and function names should be all lowercase.
tests/testthat/test_scaleListToInterval.R:4:1: style: Variable and function names should be all lowercase.
tests/testthat/test_scaleListToInterval.R:4:21: style: Variable and function names should be all lowercase.
tests/testthat/test_scaleListToInterval.R:5:1: style: Variable and function names should be all lowercase.
tests/testthat/test_scaleListToInterval.R:5:22: style: Variable and function names should be all lowercase.
tests/testthat/test_scaleListToInterval.R:8:16: style: Variable and function names should be all lowercase.
tests/testthat/test_scaleListToInterval.R:9:20: style: Variable and function names should be all lowercase.
tests/testthat/test_scaleListToInterval.R:10:20: style: Variable and function names should be all lowercase.
tests/testthat/test_scaleListToInterval.R:12:16: style: Variable and function names should be all lowercase.
tests/testthat/test_selectTranscript.R:7:10: style: Put spaces around all infix operators.
tests/testthat/test_selectTranscript.R:11:1: style: Variable and function names should be all lowercase.
tests/testthat/test_selectTranscript.R:14:10: style: Put spaces around all infix operators.
tests/testthat/test_selectTranscript.R:15:25: style: Variable and function names should be all lowercase.
tests/testthat/test_selectTranscript.R:20:10: style: Put spaces around all infix operators.
tests/testthat/test_selectTranscript.R:24:1: style: lines should not be more than 80 characters.
tests/testthat/test_selectTranscript.R:25:15: style: Use <-, not =, for assignment.
tests/testthat/test_selectTranscript.R:29:1: style: lines should not be more than 80 characters.
tests/testthat/test_selectTranscript.R:30:1: style: lines should not be more than 80 characters.
tests/testthat/test_selectTranscript.R:33:1: style: lines should not be more than 80 characters.
tests/testthat/test_selectTranscript.R:37:1: style: lines should not be more than 80 characters.
tests/testthat/test_selectTranscript.R:38:1: style: lines should not be more than 80 characters.
tests/testthat/test_utilities.R:7:10: style: Put spaces around all infix operators.
tests/testthat/test_utilities.R:18:55: style: Put spaces around all infix operators.
tests/testthat/test_utilities.R:19:55: style: Put spaces around all infix operators.
tests/testthat/test_utilities.R:21:1: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:22:1: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:26:1: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:29:10: style: Put spaces around all infix operators.
tests/testthat/test_utilities.R:30:25: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:33:1: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:55:23: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:56:23: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:61:3: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:61:41: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:62:3: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:62:41: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:66:23: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:67:23: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:74:40: style: Commas should always have a space after.
tests/testthat/test_utilities.R:74:42: style: Commas should always have a space after.
tests/testthat/test_utilities.R:78:36: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:79:36: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:86:38: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:87:38: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:92:3: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:94:32: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:96:3: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:96:52: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:100:3: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:103:9: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:106:16: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:106:32: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:110:60: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:124:12: style: Put spaces around all infix operators.
tests/testthat/test_utilities.R:144:23: style: Use <-, not =, for assignment.
tests/testthat/test_utilities.R:145:23: style: Use <-, not =, for assignment.
tests/testthat/test_utilities.R:152:1: style: lines should not be more than 80 characters.
tests/testthat/test_utilities.R:152:41: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:153:1: style: lines should not be more than 80 characters.
tests/testthat/test_utilities.R:153:41: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:158:23: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:160:47: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:163:23: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:165:47: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:168:1: style: lines should not be more than 80 characters.
tests/testthat/test_utilities.R:170:3: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:171:3: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:181:40: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:182:40: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:188:3: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:189:3: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:199:24: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:200:24: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:204:3: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:205:13: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:206:48: style: Variable and function names should be all lowercase.
tests/testthat/test_utilities.R:206:57: style: Variable and function names should be all lowercase.