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Commit 15b4c62f authored by Konrad Zych's avatar Konrad Zych
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with 26 additions and 11 deletions
......@@ -10,4 +10,3 @@ SIAMCAT.RProj
*.DS_Store*
inst/doc
*.pdf
......@@ -10,7 +10,7 @@ build:
stage: build
script:
- R CMD build ./ --no-build-vignettes
- R CMD INSTALL SIAMCAT_0.99.1.tar.gz
- R CMD INSTALL SIAMCAT_0.99.6.tar.gz
- mv SIAMCAT_* ./Rscript_flavor
- cd Rscript_flavor
- wget http://congo.embl.de/downloads/siamcat_test_data.tar.gz
......@@ -24,7 +24,7 @@ preprocess_data:
stage: preprocess_data
before_script:
- cd Rscript_flavor
- R CMD INSTALL SIAMCAT_0.99.1.tar.gz
- R CMD INSTALL SIAMCAT_0.99.6.tar.gz
script:
- Rscript 01_validate_data.r --metadata_in num_metadata_cancer-vs-healthy_study-pop-I_N141_tax_profile_mocat_bn_genus.tsv --metadata_out valMetaData.tsv --label_in label_cancer-vs-healthy_study-pop-I_N141_tax_profile_mocat_bn_genus.tsv --label_out valLabel.tsv --feat_in feat_cancer-vs-healthy_study-pop-I_N141_tax_profile_mocat_bn_genus.tsv --feat_out valFeat.tsv
- Rscript 02_select_samples.r --metadata_in valMetaData.tsv --metadata_out valMetaData_sel.tsv --label_in valLabel.tsv --label_out valLabel_sel.tsv --feat_in valFeat.tsv --feat_out valFeat_sel.tsv --filter_var="age" --allowed_range="[0,120]"
......@@ -47,7 +47,7 @@ train_model:
stage: train_model
before_script:
- cd Rscript_flavor
- R CMD INSTALL SIAMCAT_0.99.1.tar.gz
- R CMD INSTALL SIAMCAT_0.99.6.tar.gz
script:
- Rscript 09_train_models.r --feat_in valFeat_sel_norm.tsv --label_in valLabel_sel.tsv --method="lasso" --data_split dataSplit.Rdata --mlr_models_list models.RData --stratify="TRUE" --sel_criterion="auprc" --min_nonzero_coeff="2"
......@@ -64,7 +64,7 @@ make_predictions:
stage: make_predictions
before_script:
- cd Rscript_flavor
- R CMD INSTALL SIAMCAT_0.99.1.tar.gz
- R CMD INSTALL SIAMCAT_0.99.6.tar.gz
script:
- Rscript 10_make_predictions.r --label_in valLabel_sel.tsv --feat_in valFeat_sel_norm.tsv --data_split dataSplit.Rdata --pred pred.tsv --mlr_models_list models.RData
......@@ -81,9 +81,9 @@ evaluate_interpret:
stage: evaluate_interpret
before_script:
- cd Rscript_flavor
- R CMD INSTALL SIAMCAT_0.99.1.tar.gz
- R CMD INSTALL SIAMCAT_0.99.6.tar.gz
script:
- Rscript 11_evaluate_predictions.r --label_in valLabel_sel.tsv --plot evalPlot.pdf --pred pred.tsv
- Rscript 11_evaluate_predictions.r --feat_in valFeat_sel_norm.tsv --label_in valLabel_sel.tsv --plot evalPlot.pdf --pred pred.tsv
- Rscript 12_interpret_model.r --label_in valLabel_sel.tsv --feat_in valFeat_sel_norm.tsv --origin_feat valFeat_sel.tsv --metadata_in valMetaData_sel.tsv --mlr_models_list models.RData --plot interpretation.pdf --pred pred.tsv --col_scheme="BrBG" --heatmap_type="zscore" --consens_thres="0.5"
artifacts:
......
Summary
###Summary
(Summarize the bug encountered concisely)
Relevant logs and/or screenshots
###Relevant logs and/or screenshots
(Paste any relevant logs - please use code blocks (```) to format console output,
logs, and code as it's very hard to read otherwise.)
......
###Summary
(Summarize the requested feature encountered concisely)
###Affected functions/datasets/objects
(If possible, mention all functions/datasets/objects that this feature would have an effect on)
/label ~feature-request
/cc @zych
\ No newline at end of file
###Summary
### Summary
(Summarize what are you going to work on)
###Affected functions/datasets/objects
### Affected functions/datasets/objects
(If possible, mention all functions/datasets/objects that your changes will have an effect on)
### Goals/sub-features
- [ ]
/estimate 1h
/cc @zych
\ No newline at end of file
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