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getPatternGeneSet: replace pathways column with gene.set #108

Merged
merged 3 commits into from
May 29, 2024
Merged

getPatternGeneSet: replace pathways column with gene.set #108

merged 3 commits into from
May 29, 2024

Commits on May 29, 2024

  1. replace pathway column with gene.set 

    Bug found in issue #107. Creating a separate column for "gene.set" apart from the "pathways" column generated by the fgsea and fora functions led to gene set names being associated with the wrong rows. To avoid this kind of issue of redundant columns naming the gene sets that caused this bug, the pathways column is renamed to gene.set then converted to a factor ordered by adjusted p-value.
    @jmitchell81
    jmitchell81 committed May 29, 2024
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  2. test significant gene sets 

    Tests for gene set plotting now include a check for a sig_p1 gene set that should be associated with pattern 1.
    @jmitchell81
    jmitchell81 committed May 29, 2024
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  3. bump version

    @dimalvovs
    dimalvovs committed May 29, 2024
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