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Create interactive table of differential gene expression analysis results from 'K2' object

Source: R/getDGEInter.R
getDGEInter.Rd

Create interactive table differential gene expression analysis results from 'K2' object.

Usage

getDGEInter(
  K2res,
  maxFDR = 0.05,
  minDiff = NULL,
  maxPval = NULL,
  genes = NULL,
  nodes = NULL,
  pagelength = 50
)

Arguments

K2res

A K2 class object.

maxFDR

Numeric. A value between 0 and 1 indicating the FDR cutoff for differential gene expressio analysis.

minDiff

Numeric. A value between 0 and 1 indicating the mean difference cutoff for differential gene expressio analysis.

maxPval

Numeric. A value between 0 and 1 indicating the p-value cutoff for differential gene expression analysis.

genes

Character. A vector of gene identifiers to display.

nodes

Character. A vector of node identifiers to display.

pagelength

Numeric. Number of rows to display in each page of output.

Value

An interactive data frame with the following columns:

  • Gene: The identifier of the gene

  • Node: The identifier of the partition

  • Edge: The identifier of partition subgroup

  • Direction: The direction of coefficient for the assigned gene

  • P Value: The p-value estimated by differential analysis

  • FDR: The multiple hypothesis corrected FDR p-value, adjusted across all partitions

  • Diff: The difference between the means of each subgroup at a given partition

  • Mean: The mean across all observations at the given partition

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.