MetabolicFeatures¶

This process performs enrichment analysis for the metabolic pathways for each group in each subset.

The enrichment analysis is done with fgsea package or the GSEA_R package.

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 using fgsea package.
  If False, the GSEA_R package will be used.
  
• 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