R: A Function to Evaluate Gene-Set Enrichment Using PAEA.
PAEAAnalysis
R Documentation
A Function to Evaluate Gene-Set Enrichment Using PAEA.
Description
This function 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.
This input is the first part of the output from chdirAnalysis, which has the names $chdirprops. This contains the characteristic direction which forms the basis for the enrichmnet analysis.
gmtfile
A data set composed of a list of lists of genes (a GMT file); each list of genes has, as its first element, a label for the gene list that follows in that line. For example, if the genes are members of a pathway then the list will be of the form: pathway_name Gene1 Gene2 ... GeneN.
gammas
The list of shrinkage parameter values as used in the calculation of the characteristic direction.
casesensitive
A logical variable which determines whether the gene comparisons should be case sensitive.
showprogress
show a progress bar.
Value
p_values
A matrix of p values with gene sets down the rows and values of the shrinkage parameter values across the columns.
principal_angles
A matrix with rows corresponding to gene sets, columns corresponding to values of the shrinkage parameter and elements equal to the principal angle between the gene set subspace and the characteristic direction.
Author(s)
Neil R. Clark and Avi Ma'ayan
References
Clark, Neil R., et al. "The characteristic direction: a geometrical approach to identify differentially expressed genes." BMC bioinformatics 15.1 (2014): 79.
Examples
##---- Should be DIRECTLY executable !! ----
##-- ==> Define data, use random,
##-- or do help(data=index) for the standard data sets.
##################################
#
# An example PAEA analysis
#
##################################
# Load the expression data
data(example_expression_data)
data(example_sampleclass)
data(example_gammas)
#load a gmt file
data(GeneOntology_BP.gmt)
# Run the characteristic direction analysis
chdir_analysis_example <- chdirAnalysis(example_expression_data,example_sampleclass,
example_gammas,CalculateSig=FALSE)
# Run the PAEA analysis
PAEAtest <- PAEAAnalysis(chdir_analysis_example$chdirprops, gmt[1:100], example_gammas)
# Examine the p values
PAEAtest$p_values
# Examine the principal angles
PAEAtest$principal_angles
## 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/PAEAAnalysis.Rd_%03d_medium.png", width=480, height=480)
> ### Name: PAEAAnalysis
> ### Title: A Function to Evaluate Gene-Set Enrichment Using PAEA.
> ### Aliases: PAEAAnalysis
> ### Keywords: enrichment multivariate
>
> ### ** Examples
>
> ##---- Should be DIRECTLY executable !! ----
> ##-- ==> Define data, use random,
> ##-- or do help(data=index) for the standard data sets.
>
>
> ##################################
> #
> # An example PAEA analysis
> #
> ##################################
> # Load the expression data
>
> data(example_expression_data)
> data(example_sampleclass)
> data(example_gammas)
>
> #load a gmt file
> data(GeneOntology_BP.gmt)
>
> # Run the characteristic direction analysis
> chdir_analysis_example <- chdirAnalysis(example_expression_data,example_sampleclass,
+ example_gammas,CalculateSig=FALSE)
>
> # Run the PAEA analysis
>
> PAEAtest <- PAEAAnalysis(chdir_analysis_example$chdirprops, gmt[1:100], example_gammas)
| | | 0% | |= | 1% | |= | 2% | |== | 3% | |=== | 4% | |==== | 5% | |==== | 6% | |===== | 7% | |====== | 8% | |====== | 9% | |======= | 10% | |======== | 11% | |======== | 12% | |========= | 13% | |========== | 14% | |========== | 15% | |=========== | 16% | |============ | 17% | |============= | 18% | |============= | 19% | |============== | 20% | |=============== | 21% | |=============== | 22% | |================ | 23% | |================= | 24% | |================== | 25% | |================== | 26% | |=================== | 27% | |==================== | 28% | |==================== | 29% | |===================== | 30% | |====================== | 31% | |====================== | 32% | |======================= | 33% | |======================== | 34% | |======================== | 35% | |========================= | 36% | |========================== | 37% | |=========================== | 38% | |=========================== | 39% | |============================ | 40% | |============================= | 41% | |============================= | 42% | |============================== | 43% | |=============================== | 44% | |================================ | 45% | |================================ | 46% | |================================= | 47% | |================================== | 48% | |================================== | 49% | |=================================== | 50% | |==================================== | 51% | |==================================== | 52% | |===================================== | 53% | |====================================== | 54% | |====================================== | 55% | |======================================= | 56% | |======================================== | 57% | |========================================= | 58% | |========================================= | 59% | |========================================== | 60% | |=========================================== | 61% | |=========================================== | 62% | |============================================ | 63% | |============================================= | 64% | |============================================== | 65% | |============================================== | 66% | |=============================================== | 67% | |================================================ | 68% | |================================================ | 69% | |================================================= | 70% | |================================================== | 71% | |================================================== | 72% | |=================================================== | 73% | |==================================================== | 74% | |==================================================== | 75% | |===================================================== | 76% | |====================================================== | 77% | |======================================================= | 78% | |======================================================= | 79% | |======================================================== | 80% | |========================================================= | 81% | |========================================================= | 82% | |========================================================== | 83% | |=========================================================== | 84% | |============================================================ | 85% | |============================================================ | 86% | |============================================================= | 87% | |============================================================== | 88% | |============================================================== | 89% | |=============================================================== | 90% | |================================================================ | 91% | |================================================================ | 92% | |================================================================= | 93% | |================================================================== | 94% | |================================================================== | 95% | |=================================================================== | 96% | |==================================================================== | 97% | |===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 100%
>
> # Examine the p values
>
> PAEAtest$p_values
translation (GO:0006412)
[1,] 0.01499437
RNA splicing, via transesterification reactions (GO:0000375)
[1,] 0.5233092
regulation of secretion (GO:0051046)
[1,] 0.6557127
positive regulation of secretion (GO:0051047)
[1,] 0.6557127
cellular amine metabolic process (GO:0009308)
[1,] 0.8229856
signal transduction (GO:0007165) cell communication (GO:0007154)
[1,] 0.9359704 0.9657269
protein complex assembly (GO:0006461) protein secretion (GO:0009306)
[1,] 0.9900633 1
rRNA transcription (GO:0009303)
[1,] 1
positive regulation of DNA replication (GO:0045740)
[1,] 1
respiratory burst (GO:0045730)
[1,] 1
positive regulation of protein catabolic process (GO:0045732)
[1,] 1
positive regulation of DNA repair (GO:0045739)
[1,] 1
negative regulation of adenylate cyclase activity (GO:0007194)
[1,] 1
inhibition of adenylate cyclase activity by G-protein signaling (GO:0007193)
[1,] 1
regulation of transcription factor activity (GO:0051090)
[1,] 1
activation of adenylate cyclase activity (GO:0007190)
[1,] 1
positive regulation of transcription factor activity (GO:0051091)
[1,] 1
positive regulation of NF-kappaB transcription factor activity (GO:0051092)
[1,] 1
response to radiation (GO:0009314)
[1,] 1
oligosaccharide metabolic process (GO:0009311)
[1,] 1
positive regulation of glycogen biosynthetic process (GO:0045725)
[1,] 1
positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)
[1,] 1
positive regulation of binding (GO:0051099)
[1,] 1
positive regulation of translation (GO:0045727)
[1,] 1
respiratory electron transport chain (GO:0022904)
[1,] 1
amine biosynthetic process (GO:0009309)
[1,] 1
response to hydrogen peroxide (GO:0042542)
[1,] 1
translational initiation (GO:0006413)
[1,] 1
translational elongation (GO:0006414) RNA export from nucleus (GO:0006405)
[1,] 1 1
mRNA export from nucleus (GO:0006406)
[1,] 1
positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)
[1,] 1
negative regulation of cell cycle (GO:0045786)
[1,] 1
ER-associated protein catabolic process (GO:0030433)
[1,] 1
mRNA catabolic process (GO:0006402)
[1,] 1
positive regulation of cell cycle (GO:0045787)
[1,] 1
tRNA modification (GO:0006400)
[1,] 1
positive regulation of cell adhesion (GO:0045785)
[1,] 1
RNA catabolic process (GO:0006401)
[1,] 1
response to reactive oxygen species (GO:0000302)
[1,] 1
negative regulation of secretion (GO:0051048)
[1,] 1
positive regulation of ossification (GO:0045778)
[1,] 1
negative regulation of transport (GO:0051051)
[1,] 1
superoxide anion generation (GO:0042554)
[1,] 1
regulation of angiogenesis (GO:0045765)
[1,] 1
positive regulation of adenylate cyclase activity (GO:0045762)
[1,] 1
positive regulation of anti-apoptosis (GO:0045768)
[1,] 1
positive regulation of angiogenesis (GO:0045766)
[1,] 1
regulation of anti-apoptosis (GO:0045767)
[1,] 1
regulation of S phase (GO:0033261)
[1,] 1
negative regulation of hormone secretion (GO:0046888)
[1,] 1
positive regulation of lipid biosynthetic process (GO:0046889)
[1,] 1
protein folding (GO:0006457)
[1,] 1
positive regulation of hormone secretion (GO:0046887)
[1,] 1
reciprocal meiotic recombination (GO:0007131)
[1,] 1
regulation of translational initiation (GO:0006446)
[1,] 1
regulation of translation (GO:0006417)
[1,] 1
tRNA aminoacylation for protein translation (GO:0006418)
[1,] 1
meiosis (GO:0007126) phospholipid catabolic process (GO:0009395)
[1,] 1 1
protein amino acid O-linked glycosylation (GO:0006493)
[1,] 1
epidermal growth factor receptor signaling pathway (GO:0007173)
[1,] 1
regulation of epidermal growth factor receptor activity (GO:0007176)
[1,] 1
protein amino acid lipidation (GO:0006497)
[1,] 1
transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)
[1,] 1
transforming growth factor beta receptor signaling pathway (GO:0007179)
[1,] 1
ATP metabolic process (GO:0046034)
[1,] 1
spliceosomal snRNP biogenesis (GO:0000387)
[1,] 1
endothelial cell migration (GO:0043542)
[1,] 1
G-protein signaling, coupled to cyclic nucleotide second messenger (GO:0007187)
[1,] 1
protein amino acid glycosylation (GO:0006486)
[1,] 1
G-protein signaling, coupled to cAMP nucleotide second messenger (GO:0007188)
[1,] 1
protein amino acid N-linked glycosylation (GO:0006487)
[1,] 1
protein amino acid ADP-ribosylation (GO:0006471)
[1,] 1
protein amino acid dephosphorylation (GO:0006470)
[1,] 1
protein amino acid methylation (GO:0006479)
[1,] 1
leukocyte adhesion (GO:0007159)
[1,] 1
regulation of nucleocytoplasmic transport (GO:0046822)
[1,] 1
homophilic cell adhesion (GO:0007156)
[1,] 1
protein amino acid acetylation (GO:0006473)
[1,] 1
heterophilic cell adhesion (GO:0007157)
[1,] 1
positive regulation of nucleocytoplasmic transport (GO:0046824)
[1,] 1
negative regulation of cell adhesion (GO:0007162)
[1,] 1
establishment or maintenance of cell polarity (GO:0007163)
[1,] 1
cell-matrix adhesion (GO:0007160)
[1,] 1
negative regulation of protein kinase activity (GO:0006469)
[1,] 1
transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)
[1,] 1
enzyme linked receptor protein signaling pathway (GO:0007167)
[1,] 1
response to estrogen stimulus (GO:0043627)
[1,] 1
cardiac muscle contraction (GO:0060048)
[1,] 1
skeletal system development (GO:0001501) ossification (GO:0001503)
[1,] 1 1
regulation of neurotransmitter levels (GO:0001505)
[1,] 1
cell surface receptor linked signal transduction (GO:0007166)
[1,] 1.03894
protein modification process (GO:0006464) cell adhesion (GO:0007155)
[1,] 1.042983 1.054574
G-protein coupled receptor protein signaling pathway (GO:0007186)
[1,] 1.061444
protein amino acid phosphorylation (GO:0006468)
[1,] 1.063528
>
> # Examine the principal angles
>
> PAEAtest$principal_angles
translation (GO:0006412)
[1,] 0.01499437
RNA splicing, via transesterification reactions (GO:0000375)
[1,] 0.5233092
regulation of secretion (GO:0051046)
[1,] 0.6557127
positive regulation of secretion (GO:0051047)
[1,] 0.6557127
cellular amine metabolic process (GO:0009308)
[1,] 0.8229856
signal transduction (GO:0007165) cell communication (GO:0007154)
[1,] 0.9359704 0.9657269
protein complex assembly (GO:0006461) protein secretion (GO:0009306)
[1,] 0.9900633 1
rRNA transcription (GO:0009303)
[1,] 1
positive regulation of DNA replication (GO:0045740)
[1,] 1
respiratory burst (GO:0045730)
[1,] 1
positive regulation of protein catabolic process (GO:0045732)
[1,] 1
positive regulation of DNA repair (GO:0045739)
[1,] 1
negati
providing 
.
