pathwayko: performing the KO pathway enrichment analysis on single...

In allenaigit/pathwayko: PathwayKO: An R package for knock-out pathway enrichment analysis

performing the KO pathway enrichment analysis on single dataset

Description

It invokes utilities, highedges, functions and methods to calculate the scores of all edges (Hanoudi et al., 2017) in a known global KEGG graph (Zhang and Wiemann, 2009) to yield the distribution of edge scores, and thus automatically determines a change point on the distribution of edge scores by the change-point analysis method (Killick and Eckley, 2014). Outputs include the KO gene-associated sub-graph, the list of differential expression (DE) genes, and the list of true positive KO KEGG pathways. References: Hanoudi S., et al. (2017) Identifying biologically relevant putative mechanisms in a given phenotype comparison. PLoS ONE 12, e0176950; Zhang J. D. and Wiemann S. (2009) KEGGgraph: a graph approach to KEGG pathway in R and bioconductor. Bioinformatics, 25, 1470–1471; Killick R. and Eckley I. (2014) changepoint: An R package for changepoint analysis. J. Statistic Software. 58,1–19.

Usage

pathwayko()

Arguments

batch	boolean, should only be set to TRUE by pathwayko_batch function
batch_DataObject	should only be set by pathwayko_batch function
batch_uip	should only be set by pathwayko_batch function

Value

NULL if encountered error, TRUE when batch is false and an internal object with results if batch is true

allenaigit/pathwayko documentation built on Nov. 23, 2022, 5:43 p.m.