Commit bc603320 authored by Konrad Zych's avatar Konrad Zych

removing unused parameters

parent 13eaeec0
Pipeline #3032 failed with stage
in 4 minutes and 21 seconds
image: r-base
before_script:
- cd Rscript_flavor
- Rscript 00_setup.r
- cd ../
- R CMD build ./
- mv SIAMCAT*.tar.gz Rscript_flavor/.
- cd Rscript_flavor
- wget http://congo.embl.de/downloads/siamcat_test_data.tar.gz
- tar -zxf siamcat_test_data.tar.gz && rm siamcat_test_data.tar.gz
test:
stage: test
script:
- Rscript 00_setup.r
- Rscript 01_validate_data.r --srcdir .. --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 --srcdir .. --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]"
- Rscript 03_check_for_confounders.r --srcdir .. --metadata_in valMetaData_sel.tsv --plot metaCheck.pdf --label_in valLabel_sel.tsv
- Rscript 04_filter_features.r --feat_in valFeat_sel.tsv --feat_out valFeat_sel_filtered.tsv --method="abundance" --cutoff="0.001" --recomp_prop="FALSE" --rm_unmapped="TRUE"
- Rscript 05_check_associations.r --srcdir .. --feat_in valFeat_sel_filtered.tsv --label_in valLabel_sel.tsv --plot assoc.pdf --col_scheme="RdYlBu" --alpha="0.7" --min_fc="0" --mult_test="fdr" --max_show="50" --detect_limit="1e-06" --plot_type="bean"
- Rscript 06_normalize_features.r --feat_in valFeat_sel_filtered.tsv --feat_out valFeat_sel_norm.tsv --param_out param_out.tsv --method="log.unit" --log_n0="1e-08" --sd_min_quantile="0.2" --vector_norm="2" --norm_margin="1"
- Rscript 07_add_metadata_as_predictor.r --feat_in valFeat_sel_norm.tsv --feat_out valFeat_sel_norm.tsv --metadata_in valMetaData_sel.tsv --pred_names="fobt" --std_meta="TRUE"
- Rscript 08_split_data.r --srcdir .. --label_in valLabel_sel.tsv --train_sets trainSets.tsv --test_sets testSets.tsv --num_folds="10" --resample="5" --stratify="TRUE" --inseparable="NULL" --metadata_in valMetaData_sel.tsv
- Rscript 09_train_models.r --srcdir .. --feat_in valFeat_sel_norm.tsv --label_in valLabel_sel.tsv --method="lasso" --train_sets trainSets.tsv --mlr_models_list models.RData --stratify="TRUE" --sel_criterion="auprc" --min_nonzero_coeff="2"
- Rscript 10_make_predictions.r --srcdir .. --label_in valLabel_sel.tsv --feat_in valFeat_sel_norm.tsv --test_sets testSets.tsv --pred pred.tsv --mlr_models_list models.RData
- Rscript 11_evaluate_predictions.r --srcdir .. --label_in valLabel_sel.tsv --plot evalPlot.pdf --pred pred.tsv
- Rscript 12_interpret_model.r --srcdir .. --label_in valLabel_sel.tsv --feat valFeat_sel_norm.tsv --origin_feat valFeat_sel.tsv --meta valMetaData_sel.tsv --model models.RData --plot interpretation.pdf --pred pred.tsv --col_scheme="BrBG" --heatmap_type="zscore" --consens_thres="0.5"
only:
- master
- development
after_script:
- rm -r *.tsv
- echo "cleaned up"
\ No newline at end of file
......@@ -20,7 +20,7 @@ suppressMessages(library('SIAMCAT'))
option_list = list(
#make_option('--pkgdir', type='character', help='Source directory of dataprep'),
make_option(c('-s', '--srcdir'), type='character', help='Source directory of this and other utility scripts'),
make_option('--label', type='character', help='Input file containing labels'),
make_option('--label_in', type='character', help='Input file containing labels'),
make_option('--pred', type='character', help='Input file containing the trained classification model(s)'),
make_option('--plot', type='character', help='Output file for plotting'),
make_option('--write_eval_results', type='logical', default=FALSE, help='Should calculated parameters be written into tab-delimited file? (Necessary for generation of test files'),
......@@ -32,7 +32,7 @@ opt <- parse_args(OptionParser(option_list=option_list))
cat("=== 11_model_evaler.r\n")
cat("=== Paramaters of the run:\n\n")
cat('srcdir =', opt$srcdir, '\n')
cat('label =', opt$label, '\n')
cat('label_in =', opt$label_in, '\n')
cat('pred =', opt$pred, '\n')
cat('plot =', opt$plot, '\n')
cat('write_eval_results =', opt$write_eval_results, '\n')
......@@ -42,7 +42,7 @@ cat('\n')
### If variable source.dir does not end with "/", append "/" to end of source.dir
source.dir <- appendDirName(opt$srcdir)
start.time <- proc.time()[1]
label <- read.labels(opt$label)
label <- read.labels(opt$label_in)
pred <- read.table(file=opt$pred, sep='\t', header=TRUE, row.names=1, check.names=FALSE, comment.char="#")
......
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