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Updated the test suite for the GSEA Desktop 4.2.0 bugfix release
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50 changes: 50 additions & 0 deletions
50
gpunit_functionality/collapse/collapse_NaN_Missing_max_test.yml
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# Copyright (c) 2003-2021 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved. | ||
#module: urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00072:20 | ||
module: GSEA | ||
name: GSEA collapse_NaN_Missing_max_test | ||
description: Test the GSEA 'collapse dataset' function handling NaN and Missing values, collapse to max of probes. Tests are centered on HTR4, HTR7, NPAL2, NPAL3, GSTK1. | ||
params: | ||
expression.dataset: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes_hgu133a_NaN_missing_vals.gct" | ||
gene.sets.database: [ "<%gpunit.testData%>gpunit/GSEA/v20/input/c1.symbols.reduced.gmt" ] | ||
number.of.permutations: "10" | ||
# Uses P53_6samples.cls because it happens to have a reasonable class template for this use | ||
phenotype.labels: "<%gpunit.testData%>gpunit/GSEA/v20/input/P53_6samples.cls" | ||
target.profile: "" | ||
permutation.type: "phenotype" | ||
collapse.dataset: "Collapse" | ||
chip.platform.file: "<%gpunit.testData%>gpunit/GSEA/v20/input/HG_U133A.chip" | ||
# Modifying the ZIP name here so that the diffCmd can find the RNK inside. We could modify the diffCmd | ||
# to be able to find it, but that makes the code somewhat complicated. | ||
output.file.name: "Diabetes_hgu133a_NaN_missing_vals_collapsed_to_symbols.zip" | ||
scoring.scheme: "weighted" | ||
metric.for.ranking.genes: "Signal2Noise" | ||
gene.list.sorting.mode: "real" | ||
gene.list.ordering.mode: "descending" | ||
max.gene.set.size: "500" | ||
min.gene.set.size: "15" | ||
collapsing.mode.for.probe.sets.with.more.than.one.match: "Max_probe" | ||
normalization.mode: "meandiv" | ||
randomization.mode: "no_balance" | ||
omit.features.with.no.symbol.match: "true" | ||
median.for.class.metrics: "false" | ||
number.of.markers: "100" | ||
# Note that we use a fixed random seed rather than the 'timestamp' default so that we'll have reproducible test results | ||
random.seed: "149" | ||
create.svgs: "false" | ||
create.gcts: "true" | ||
save.random.ranked.lists: "false" | ||
plot.graphs.for.the.top.sets.of.each.phenotype: "20" | ||
make.detailed.gene.set.report: "false" | ||
selected.gene.sets: "" | ||
dev.mode: "true" | ||
alt.delim: "" | ||
create.zip: "true" | ||
assertions: | ||
jobStatus: success | ||
files: | ||
"Diabetes_hgu133a_NaN_missing_vals_collapsed_to_symbols.zip": | ||
diffCmd: ../diffGseaResults.sh | ||
diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/collapse/collapse_NaN_Missing_max_test/Diabetes_hgu133a_NaN_missing_vals_collapsed_to_symbols.zip" | ||
"stdout.txt": | ||
diffCmd: ../grepMessages.sh | ||
diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/collapse/collapse_NaN_Missing_max_test/stdoutMatches.txt" |
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# Copyright (c) 2003-2021 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved. | ||
#!/bin/sh | ||
|
||
# The file passed in $1 should be a list of fixed strings, one per line, to be checked if they are found in the $2 file. | ||
# We verify by checking the count of matches against the count of fixed strings/ | ||
# This is an imperfect check but should be good enough provided the fixed strings are sufficiently detailed to appear | ||
# only *once* in the $2 file. | ||
grepOut=`grep -c -F -f $1 $2` | ||
numChecks=`cat $1 | wc -l` | ||
exit $(( numChecks - grepOut )) |
51 changes: 51 additions & 0 deletions
51
gpunit_functionality/metrics/continuous_metric_NaN_Missing_test.yml
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# Copyright (c) 2003-2021 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved. | ||
#module: urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00072:20 | ||
module: GSEA | ||
name: GSEA continuous_metric_NaN_Missing_test | ||
description: Test the GSEA continuous metric handling NaN and Missing values. Tests are centered on HTR4, HTR7, NPAL2, NPAL3, GSTK1. | ||
params: | ||
# Using a dataset needing collapse because it happens to have missing & NaN values | ||
expression.dataset: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes_hgu133a_NaN_missing_vals.gct" | ||
gene.sets.database: [ "<%gpunit.testData%>gpunit/GSEA/v20/input/c1.symbols.reduced.gmt" ] | ||
number.of.permutations: "10" | ||
phenotype.labels: "<%gpunit.testData%>gpunit/GSEA/v20/input/Diabetes_6samples_fake_as_cont_pheno.cls" | ||
target.profile: "" | ||
permutation.type: "phenotype" | ||
collapse.dataset: "Collapse" | ||
chip.platform.file: "<%gpunit.testData%>gpunit/GSEA/v20/input/HG_U133A.chip" | ||
# Modifying the ZIP name here so that the diffCmd can find the RNK inside. We could modify the diffCmd | ||
# to be able to find it, but that makes the code somewhat complicated. | ||
output.file.name: "Diabetes_hgu133a_NaN_missing_vals_collapsed_to_symbols.zip" | ||
scoring.scheme: "weighted" | ||
metric.for.ranking.genes: "Spearman" | ||
gene.list.sorting.mode: "real" | ||
gene.list.ordering.mode: "descending" | ||
max.gene.set.size: "500" | ||
min.gene.set.size: "15" | ||
collapsing.mode.for.probe.sets.with.more.than.one.match: "Max_probe" | ||
normalization.mode: "meandiv" | ||
randomization.mode: "no_balance" | ||
omit.features.with.no.symbol.match: "true" | ||
median.for.class.metrics: "false" | ||
number.of.markers: "100" | ||
# Note that we use a fixed random seed rather than the 'timestamp' default so that we'll have reproducible test results | ||
random.seed: "149" | ||
create.svgs: "false" | ||
create.gcts: "true" | ||
save.random.ranked.lists: "false" | ||
plot.graphs.for.the.top.sets.of.each.phenotype: "20" | ||
make.detailed.gene.set.report: "false" | ||
selected.gene.sets: "" | ||
dev.mode: "true" | ||
alt.delim: "" | ||
create.zip: "true" | ||
assertions: | ||
jobStatus: success | ||
files: | ||
"Diabetes_hgu133a_NaN_missing_vals_collapsed_to_symbols.zip": | ||
diffCmd: ../diffGseaResults.sh | ||
diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/metrics/continuous_metric_NaN_Missing_test/Diabetes_hgu133a_NaN_missing_vals_collapsed_to_symbols.zip" | ||
"stdout.txt": | ||
diffCmd: ../grepMessages.sh | ||
diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/metrics/continuous_metric_NaN_Missing_test/stdoutMatches.txt" | ||
|
44 changes: 44 additions & 0 deletions
44
gpunit_functionality/metrics/metric_Diff_of_Classes_test.yml
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# Copyright (c) 2003-2021 Broad Institute, Inc., Massachusetts Institute of Technology, and Regents of the University of California. All rights reserved. | ||
#module: urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00072:20 | ||
module: GSEA | ||
name: GSEA metric_Diff_of_Classes_test | ||
description: Test GSEA using the Diff_of_Classes metric. Variation of user_gene_set_test with a reduced dataset. | ||
params: | ||
expression.dataset: "<%gpunit.testData%>gpunit/GSEA/v20/input/P53_14samples_collapsed_symbols.gct" | ||
gene.sets.database: [ "<%gpunit.testData%>gpunit/GSEA/v20/input/c1.symbols.reduced.gmt" ] | ||
number.of.permutations: "10" | ||
phenotype.labels: "<%gpunit.testData%>gpunit/GSEA/v20/input/P53_14samples.cls" | ||
target.profile: "" | ||
permutation.type: "phenotype" | ||
collapse.dataset: "No_Collapse" | ||
#chip.platform.file: | ||
output.file.name: "<expression.dataset_basename>.zip" | ||
scoring.scheme: "weighted" | ||
metric.for.ranking.genes: "Diff_of_Classes" | ||
gene.list.sorting.mode: "real" | ||
gene.list.ordering.mode: "descending" | ||
max.gene.set.size: "500" | ||
min.gene.set.size: "15" | ||
collapsing.mode.for.probe.sets.with.more.than.one.match: "Max_probe" | ||
normalization.mode: "meandiv" | ||
randomization.mode: "no_balance" | ||
omit.features.with.no.symbol.match: "true" | ||
median.for.class.metrics: "false" | ||
number.of.markers: "100" | ||
# Note that we use a fixed random seed rather than the 'timestamp' default so that we'll have reproducible test results | ||
random.seed: "149" | ||
create.svgs: "false" | ||
create.gcts: "false" | ||
save.random.ranked.lists: "false" | ||
plot.graphs.for.the.top.sets.of.each.phenotype: "20" | ||
make.detailed.gene.set.report: "false" | ||
selected.gene.sets: "" | ||
dev.mode: "true" | ||
alt.delim: "" | ||
create.zip: "true" | ||
assertions: | ||
jobStatus: success | ||
files: | ||
"P53_14samples_collapsed_symbols.zip": | ||
diffCmd: ../diffGseaResults.sh | ||
diff: "<%gpunit.resultData%>gpunit/GSEA/v20/output/metrics/metric_Diff_of_Classes_test/P53_14samples_collapsed_symbols.zip" |
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