dgrapov

#------------------------------------------------------
# demonstration of making edge lists for 
# correlation network analysis 
# by Dmitry Grapov
# 031814
#------------------------------------------------------

# load devium library for all functions
source("http://pastebin.com/raw.php?i=JVyTrYRD") # sources function to download github repo (https://github.com/dgrapov/devium)

dgrapov

Name	KEGG id
Carnitine	C00318
catechin	C06562
threonine	C00188
threonic acid	C01620
phenylethylamine	C05332
phenylalanine	C00079
N-acetyl-L-ornithine	C00437
mannitol	C00392
glutathione	C00051

dgrapov

sourceName 	sourceKEGG	sourceCID	targetName	targetKEGG	targetCID	indirect
arachidonic_acid	C00219	444899	TXB2	C05963	5283137	y
arachidonic_acid	C00219	444899	PGE2	C00584	5280360	y
arachidonic_acid	C00219	444899	LTB4	C02165	5280492	y
linoleic_acid	C01595	5280450	9,10,13-TriHOME	C14835	5282965	y
linoleic_acid	C01595	5280450	9,12,13-TriHOME	C14833	9858729	y
linoleic_acid	C01595	5280450	EKODE		5283007	y
arachidonic_acid	C00219	444899	11(12)-EpETrE		53480479	n
arachidonic_acid	C00219	444899	11-HETE	C14780	5283168	n
arachidonic_acid	C00219	444899	12-HETE	C14777	5283155	n

dgrapov

library(shiny)
library(ggvis)

shinyApp(
  ui =bootstrapPage(
    actionButton("randomize", "Randomize"),  
    ggvisOutput("plot1"),
    ggvisOutput("plot2"),
    verbatimTextOutput("summary")
  ),

dgrapov

#R code, testing RECA with the iris data
library(RECA)  

#test data
data(iris)
x<-iris[,-5] 
y<-iris$Species

#similar groups (species) in each chunk (n=3)
chunksvec<-as.numeric(y)

dgrapov

#test
test<-function(){print("hello world!")}

dgrapov

#purpose: model the relationship between effects size, sample size and power 
# holding the significance level constant (p = 0.05) for three of the most common statistical tests:
# 1) t-Test (two-sample)

# then visualize the results for medium small, medium and large effect sizes (0.2,0.5,0.8 ; http://www.uccs.edu/lbecker/effect-size.html)

#Need pwr package
if(!require(pwr)){install.packages("pwr");library("pwr")}

# t-TEST

dgrapov

#load devium (or any other package) from github repo
source.git.hub<-function(url = "https://github.com/dgrapov/devium/tree/master/R")
 {
		 if(require(RCurl)==FALSE){install.packages("RCurl");library(RCurl)} else { library(RCurl)}
		 
		#get the names of all scripts to source
		obj<-getURL("https://github.com/dgrapov/devium/tree/master/R",ssl.verifypeer=FALSE)
		tmp<-strsplit(obj,'href=\"/')
		tmp2<-unlist(strsplit(as.character(unlist(tmp)),'class'))
		scripts<-gsub("/blob","",gsub('\" ',"",tmp2[grep("dgrapov/devium/blob/master/R/",tmp2)])) # fix formatting

dgrapov

689043	 C01197
6443013	 C14762
6443013	 C14762
6446027	 C14765
6446027	 C14765
11954058	 C14813
6439873	 C16326
6439873	 C16326
1004	C00009
1023	C00013

dgrapov

C00005  C00006
C00003	C00004
C00002	C00008
C00019	C00021
C00007	C00027
C00010	C00024
C00002	C00020
C00002	C00013
C00002	C00009
C00015	C00029