A Function to Evaluate Gene-Set Enrichment Using PAEA Over Multiple GMT Files.

Description

This is a wrapper function for PAEAAnalysis which evaluates the enrichmnet of gene sets in expression data using the PAEA method. A characteristic direction (the result of the function chdirAnalysis and a Gene Matrix Transposed (GMT) file, which is a set of subsets of genes whose enrichmnet is evaluated, and returns a prioritized list of the gene sets.

Ths function takes multiple GMT files as input and output the results to Tab Separated Value files.

Usage

multigmtPAEAAnalysis(chdirresults, gmtfiles=AllGMTfiles, gammas = c(1), 
casesensitive = FALSE, showprogress=TRUE)

Arguments

Value

Author(s)

Neil R. Clark and Avi Ma'ayan

References

Clark, Neil R., et al. "The characteristic direction: a geometrical approach to identify differentially expressed genes." BMC bioinformatics 15.1 (2014): 79.

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.


##################################
#
# An example multigmtPAEA analysis
#
##################################
# Load the expression data

data(example_expression_data)
data(example_sampleclass)
data(example_gammas)

#load GMT file names
data(AllGMTfiles)

# Run the characteristic direction analysis
chdir_analysis_example <- chdirAnalysis(example_expression_data,example_sampleclass,
example_gammas,CalculateSig=FALSE)

# Run the PAEA analysis over the first two GMT files in the library

multiPAEAtest <- multigmtPAEAAnalysis(chdir_analysis_example$chdirprops, 
AllGMTfiles[2:3], example_gammas)

# To run on all the gmt files

#multiPAEAtestAll <- multigmtPAEAAnalysis(chdir_analysis_example$chdirprops, gammas=example_gammas)

## The function is currently defined as
function (chdirresults, gmtfile, gammas = c(1), casesensitive = FALSE) 
{
    gmtlinenames <- lapply(gmtfile, function(x) x[[1]])
    gmtlines <- lapply(gmtfile, function(x) x[-1])
    PAEAresults <- lapply(gmtlines, function(x) PAEA(chdirresults[[1]], 
        x, casesensitive = casesensitive))
    gammalabels <- unlist(lapply(gammas, function(x) paste("gamma=", 
        x)))
    pvalues <- lapply(PAEAresults, function(x) x[[2]])
    pvalues <- matrix(unlist(pvalues), ncol = length(gmtlines), 
        dimnames = list(gammalabels, gmtlinenames))
    pavalues <- lapply(PAEAresults, function(x) x[[1]])
    pavalues <- matrix(unlist(pvalues), ncol = length(gmtlines), 
        dimnames = list(gammalabels, gmtlinenames))
    gmtp <- sort.list(pvalues[1, ])
    list(t(pvalues[, gmtp]), t(pavalues[, gmtp]))
  }

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(GeoDE)
Loading required package: Matrix
Loading required package: MASS
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/GeoDE/multigmtPAEAAnalysis.Rd_%03d_medium.png", width=480, height=480)
> ### Name: multigmtPAEAAnalysis
> ### Title: A Function to Evaluate Gene-Set Enrichment Using PAEA Over
> ###   Multiple GMT Files.
> ### Aliases: multigmtPAEAAnalysis
> ### Keywords: enrichment multivariate
> 
> ### ** Examples
> 
> ##---- Should be DIRECTLY executable !! ----
> ##-- ==>  Define data, use random,
> ##--	or do  help(data=index)  for the standard data sets.
> 
> 
> ##################################
> #
> # An example multigmtPAEA analysis
> #
> ##################################
> # Load the expression data
> 
> data(example_expression_data)
> data(example_sampleclass)
> data(example_gammas)
> 
> #load GMT file names
> data(AllGMTfiles)
> 
> # Run the characteristic direction analysis
> chdir_analysis_example <- chdirAnalysis(example_expression_data,example_sampleclass,
+ example_gammas,CalculateSig=FALSE)
> 
> # Run the PAEA analysis over the first two GMT files in the library
> 
> multiPAEAtest <- multigmtPAEAAnalysis(chdir_analysis_example$chdirprops, 
+ AllGMTfiles[2:3], example_gammas)
   |                                                                               |                                                                      |   0%[1] 0
[1] 1
   |                                                                               |===================================                                   |  50%
> 
> # To run on all the gmt files
> 
> #multiPAEAtestAll <- multigmtPAEAAnalysis(chdir_analysis_example$chdirprops, gammas=example_gammas)
> 
> ## The function is currently defined as
> function (chdirresults, gmtfile, gammas = c(1), casesensitive = FALSE) 
+ {
+     gmtlinenames <- lapply(gmtfile, function(x) x[[1]])
+     gmtlines <- lapply(gmtfile, function(x) x[-1])
+     PAEAresults <- lapply(gmtlines, function(x) PAEA(chdirresults[[1]], 
+         x, casesensitive = casesensitive))
+     gammalabels <- unlist(lapply(gammas, function(x) paste("gamma=", 
+         x)))
+     pvalues <- lapply(PAEAresults, function(x) x[[2]])
+     pvalues <- matrix(unlist(pvalues), ncol = length(gmtlines), 
+         dimnames = list(gammalabels, gmtlinenames))
+     pavalues <- lapply(PAEAresults, function(x) x[[1]])
+     pavalues <- matrix(unlist(pvalues), ncol = length(gmtlines), 
+         dimnames = list(gammalabels, gmtlinenames))
+     gmtp <- sort.list(pvalues[1, ])
+     list(t(pvalues[, gmtp]), t(pavalues[, gmtp]))
+   }
function (chdirresults, gmtfile, gammas = c(1), casesensitive = FALSE) 
{
    gmtlinenames <- lapply(gmtfile, function(x) x[[1]])
    gmtlines <- lapply(gmtfile, function(x) x[-1])
    PAEAresults <- lapply(gmtlines, function(x) PAEA(chdirresults[[1]], 
        x, casesensitive = casesensitive))
    gammalabels <- unlist(lapply(gammas, function(x) paste("gamma=", 
        x)))
    pvalues <- lapply(PAEAresults, function(x) x[[2]])
    pvalues <- matrix(unlist(pvalues), ncol = length(gmtlines), 
        dimnames = list(gammalabels, gmtlinenames))
    pavalues <- lapply(PAEAresults, function(x) x[[1]])
    pavalues <- matrix(unlist(pvalues), ncol = length(gmtlines), 
        dimnames = list(gammalabels, gmtlinenames))
    gmtp <- sort.list(pvalues[1, ])
    list(t(pvalues[, gmtp]), t(pavalues[, gmtp]))
}
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>