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Add orgDB and pca_NA to other test config
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Addimator committed Aug 1, 2024
1 parent 6bc7936 commit 419705b
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5 changes: 5 additions & 0 deletions .test/three_prime/config/config.yaml
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Expand Up @@ -97,6 +97,8 @@ enrichment:
# pathway database to use in SPIA, needs to be available for
# the species specified by resources -> ref -> species above
pathway_database: "panther"
# OrgDB Genome wide annotation package (https://www.bioconductor.org/packages/release/BiocViews.html#___OrgDb) for the species under consideration. Only required if you want to have a gene analysis for your pathways. Else NA
orgDb: org.Hs.eg.db

meta_comparisons:
# comparison is only run if set to `true`
Expand Down Expand Up @@ -124,6 +126,9 @@ bootstrap_plots:
# for now, this will plot the sleuth-normalised kallisto count estimations with kallisto
# for all the transcripts of the respective genes

# If include_na is set to true, samples with NA values in the specified covariate column will be removed;
pca_exclude_NAs: false

plot_vars:
# significance level used for plot_vars() plots
sig_level: 0.1
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