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Perform differential analysis between subgroups at each partition

Source: R/runDGEmods.R
runDGEmods.Rd

Adds differential analysis results to the output of K2tax().

Usage

runDGEmods(
  K2res,
  DGEmethod = NULL,
  DGEexpThreshold = NULL,
  vehicle = NULL,
  variables = NULL,
  block = NULL,
  logCounts = NULL
)

Arguments

DGEmethod

Character. Method for running differential gene expression analyses. Use one of either 'limma' (default) or 'mast'.

DGEexpThreshold

Numeric. A value between 0 and 1 indicating for filtering lowly expressed genes for partition-specific differential gene expression. Proportion of observations with counts > 0 in at least one subgroup at a specific partition.

vehicle

The value in the cohort variable that contains the ID of observation to use as control. Default NULL if no vehicle to be used.

variables

Character. Columns in meta data of 'object' to control for in differential analyses.

block

Character. Block parameter in limma for modeling higherarchical data structure, such as multiple observations per individual.

logCounts

Logical. Whether or not expression values are log-scale counts or log normalized counts from RNA-seq. Default is TRUE.

Value

An object of class K2.

References

Reed ER, Monti S (2021). “Multi-resolution characterization of molecular taxonomies in bulk and single-cell transcriptomics data.” Nucleic Acids Research. doi:10.1093/nar/gkab552 , https://pubmed.ncbi.nlm.nih.gov/34226941/. Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK (2015). “limma powers differential expression analyses for RNA-sequencing and microarray studies.” Nucleic Acids Research, 43(7), e47--e47. ISSN 1362-4962, 0305-1048, doi:10.1093/nar/gkv007 , http://academic.oup.com/nar/article/43/7/e47/2414268/limma-powers-differential-expression-analyses-for. Benjamini Y, Hochberg Y (1995). “Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing.” Journal of the Royal Statistical Society: Series B (Methodological), 57(1), 289--300. ISSN 00359246, doi:10.1111/j.2517-6161.1995.tb02031.x , http://doi.wiley.com/10.1111/j.2517-6161.1995.tb02031.x.