MSEA.KDA.onestep: Run MSEA and/or KDA in one step

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/msea.kda.onestep.R

Description

MSEA.KDA.onestep performs Marker Set Enrichment Analysis (MSEA) and/or Key Driver Anlaysis (KDA) processes in one step.

Usage

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MSEA.KDA.onestep(plan, apply.MSEA=TRUE, apply.KDA=FALSE, 
maxoverlap.genesets=0.33, symbol.transfer.needed=FALSE, 
sym.from=c("HUMAN", "MOUSE"), sym.to=c("HUMAN", "MOUSE"))

Arguments

plan

a data list including file and parameter settings for MSEA and/or KDA processes:

label: unique identifier for the analysis
folder: output folder for results
modfile: path to module file (cols: MODULE GENE) 
genfile: path to gene file (cols: GENE LOCUS) (MSEA-specific)
marfile: path to marker file (cols: MARKER VALUE) (MSEA-specific)
inffile: path to module info file (cols: MODULE DESCR)
seed: seed for random number generator
permtype: gene for gene-level, locus for marker-level
nperm: max number of random permutations
mingenes: min number of genes per module (after merging)
maxgenes: max number of genes per module
quantiles: cutoffs for test statistic
maxoverlap: max overlap allowed between genes
netfile:  path to network file (TAIL HEAD WEIGHT) (KDA-specific)
apply.MSEA

determines whether MSEA will be performed to the given set. Default value is TRUE.

apply.KDA

determines whether KDA will be performed to the given set. Default value is FALSE.

maxoverlap.genesets

maximum overlapping ratio for the genesets. This is applicable if KDA is performed following the MSEA process in one-step running. Default value is 0.33.

symbol.transfer.needed

determines whether gene symbols in the gene sets are needed to be transformed between different species. Default value is FALSE.

sym.from

defines the species, whose gene symbols will be converted to the gene symbols of sym.to species. It can be either HUMAN or MOUSE. It is applicable if symbol.transfer.needed is TRUE.

sym.to

defines the species, whose gene symbols will be converted from the gene symbols of sym.from species. It can be either HUMAN or MOUSE. It is applicable if symbol.transfer.needed is TRUE.

Details

MSEA.KDA.onestep performs MSEA and/or KDA operations in one built-in function. Users can run both MSEA and KDA sequentially, or they can run either MSEA or KDA in one step with the same function. If MSEA and KDA will be applied sequentially, significantly enriched gene sets (having FDR < 0.25), coming from MSEA results, will be merged if their overlapping ratios are larger than a given threshold, i.e. maxoverlap.genesets, to proceed the next step with relatively indepent gene sets. Then, KDA is applied to this relatively independent gene sets.

Value

plan

the updated data frame after performing MSEA and/or KDA. If MSEA is performed, results will include standard MSEA results (see ssea.analyze for details); if KDA is applied, results will include standard KDA results (see kda.analyze for details).

Author(s)

Zeyneb Kurt

References

Shu L, Zhao Y, Kurt Z, Byars SG, Tukiainen T, Kettunen J, Orozco LD, Pellegrini M, Lusis AJ, Ripatti S, Zhang B, Inouye M, Makinen V-P, Yang X. Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems. BMC genomics. 2016;17(1):874.

See Also

ssea.analyze, kda.analyze

Examples

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plan <- list()
plan$label <- "hdlc"
plan$folder <- "Results"
plan$genfile <- system.file("extdata", 
"genes.hdlc_040kb_ld70.human_eliminated.txt", package="Mergeomics")
plan$marfile <- system.file("extdata", 
"marker.hdlc_040kb_ld70.human_eliminated.txt", package="Mergeomics")
plan$modfile <- system.file("extdata", 
"modules.mousecoexpr.liver.human.txt", package="Mergeomics")
plan$inffile <- system.file("extdata", 
"coexpr.info.txt", package="Mergeomics")
plan$nperm <- 100 ## default value is 20000
plan <- MSEA.KDA.onestep(plan, apply.MSEA=TRUE)

Mergeomics documentation built on Nov. 8, 2020, 6:58 p.m.