highedges: calculating edge scores, determining the change-point and...
In allenaigit/pathwayko: PathwayKO: An R package for knock-out pathway enrichment analysis
highedges R Documentation
calculating edge scores, determining the change-point and generating the KO-gene associated sub-graph
Description
It is not executed itself, instead, it is invoked by pathwayko.
Usage
highedges(
KEGGgraph = NULL,
DataObject = NULL,
condition_FC = NULL,
condition_pVal = NULL,
mc.cores = 1
)
Arguments
KEGGgraph
graphical representation of pathways in KEGG
DataObject
Object generated by calling preprocess.R
condition_FC
named list of logFC of all genes in DataObject
condition_pVal
named list of adjusted pval of all genes in DataObject
mc.cores
number of cores to be used in parallel lapply
Details
Reference: Hanoudi S., et al. (2017) Identifying biologically relevant putative mechanisms in a given phenotype comparison. PLoS ONE 12, e0176950.
Value
various information grouped together as a list
Author(s)
Original implementation by Samer Hanoudi and Sorin Draghici, modification by Hannan Ai
allenaigit/pathwayko documentation built on Nov. 23, 2022, 5:43 p.m.
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| highedges | R Documentation |
calculating edge scores, determining the change-point and generating the KO-gene associated sub-graph
Description
It is not executed itself, instead, it is invoked by pathwayko.
Usage
highedges( KEGGgraph = NULL, DataObject = NULL, condition_FC = NULL, condition_pVal = NULL, mc.cores = 1 )
Arguments
KEGGgraph |
graphical representation of pathways in KEGG |
DataObject |
Object generated by calling preprocess.R |
condition_FC |
named list of logFC of all genes in DataObject |
condition_pVal |
named list of adjusted pval of all genes in DataObject |
mc.cores |
number of cores to be used in parallel lapply |
Details
Reference: Hanoudi S., et al. (2017) Identifying biologically relevant putative mechanisms in a given phenotype comparison. PLoS ONE 12, e0176950.
Value
various information grouped together as a list
Author(s)
Original implementation by Samer Hanoudi and Sorin Draghici, modification by Hannan Ai
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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