MetabolicFeaturesIntraSubset¶

Intra-subset metabolic features - Enrichment analysis in details

Similar to the MetabolicFeatures process, this process performs enrichment analysis for the metabolic pathways for each subset in each group, instead of each group in each subset.

Environment Variables¶

• ncores (type=int;pgarg): Default: 1.
  Number of cores to use for parallelization Defaults to ScrnaMetabolicLandscape.ncores
• fgsea (flag): Default: True.
  Whether to do fast gsea analysis
• prerank_method (choice): Default: signal_to_noise.
  Method to use for gene preranking Signal to noise: the larger the differences of the means (scaled by the standard deviations); that is, the more distinct the gene expression is in each phenotype and the more the gene acts as a “class marker.”.
  Absolute signal to noise: the absolute value of the signal to noise.
  T test: Uses the difference of means scaled by the standard deviation and number of samples.
  Ratio of classes: Uses the ratio of class means to calculate fold change for natural scale data.
  Diff of classes: Uses the difference of class means to calculate fold change for nature scale data Log2 ratio of classes: Uses the log2 ratio of class means to calculate fold change for natural scale data. This is the recommended statistic for calculating fold change for log scale data.
  
  • signal_to_noise: Signal to noise
  • s2n: Alias of signal_to_noise
  • abs_signal_to_noise: absolute signal to noise
  • abs_s2n: Alias of abs_signal_to_noise
  • t_test: T test
  • ratio_of_classes: Also referred to as fold change
  • diff_of_classes: Difference of class means
  • log2_ratio_of_classes: Log2 ratio of class means
• top (type=int): Default: 10.
  N top of enriched pathways to show
• gmtfile (pgarg): The GMT file with the metabolic pathways.
  Defaults to ScrnaMetabolicLandscape.gmtfile
• grouping (type=auto;pgarg;readonly): Defines the basic groups to investigate the metabolic activity.
  Defaults to ScrnaMetabolicLandscape.grouping
• grouping_prefix (type=auto;pgarg;readonly): Default: "".
  Working as a prefix to group names.
  Defaults to ScrnaMetabolicLandscape.grouping_prefix
• subsetting (type=auto;pgarg;readonly): How do we subset the data.
  Another column(s) in the metadata.
  Defaults to ScrnaMetabolicLandscape.subsetting
• subsetting_prefix (type=auto;pgarg;readonly): Working as a prefix to subset names.
  Defaults to ScrnaMetabolicLandscape.subsetting_prefix
• subsetting_comparison (type=json;pgarg;readonly): Default: {}.
  How do we compare the subsets.
  Defaults to ScrnaMetabolicLandscape.subsetting_comparison