## ----setup, include=F, echo=F, message= FALSE----------------------------
knitr::opts_chunk$set(fig.width=4, fig.height=4, fig.pos = "h", tidy = TRUE, tidy.opts=list(width.cutoff=60))
## ----include=F, echo=F---------------------------------------------------
packages <- c("NEArender","data.table","graphics","tinytex")
if (length(setdiff(packages, rownames(installed.packages()))) > 0) {
install.packages(setdiff(packages, rownames(installed.packages())),repos = "http://cran.us.r-project.org")
}
## ----include=F-----------------------------------------------------------
library(NEArender)
library(data.table)
library(graphics)
library(tinytex)
## ------------------------------------------------------------------------
# input <- fread("http://research.scilifelab.se/andrej_alexeyenko/downloads/test_data/FANTOM5.43samples.txt",
# sep="\t",header=T,stringsAsFactors=FALSE,data.table = F)
## Converting genenames as rownames
# rownames(input) <-input[,1]
# input <- as.matrix(input[,c(2:ncol(input))])
data("fantom5.43samples")
input <- fantom5.43samples
dim(input)
ags.list1 <- samples2ags(input, Ntop=20, method="topnorm")
## ------------------------------------------------------------------------
data("tcga.gbm",package="NEArender")
ags.list3 <- mutations2ags(tcga.gbm, col.mask="[-.]01$")
## ------------------------------------------------------------------------
ags.list2 <-import.gs("http://research.scilifelab.se/andrej_alexeyenko/downloads/test_data/cluster2_Downregulated_ags.txt", Lowercase = 1, col.gene = 1,col.set = 3, gs.type = 'ags')
## ------------------------------------------------------------------------
fgs.list <- import.gs("http://research.scilifelab.se/andrej_alexeyenko/downloads/test_data/can.sig.go.txt",
Lowercase = 1, col.gene = 2, col.set = 3, gs.type = 'fgs')
## ------------------------------------------------------------------------
data(can.sig.go)
fgs.list <- import.gs(can.sig.go)
## ------------------------------------------------------------------------
data(net.kegg)
net <- import.net(net.kegg)
print(paste(names(net$links)[10], net$links[[10]], sep=": "))
## ------------------------------------------------------------------------
net <- import.net("http://research.scilifelab.se/andrej_alexeyenko/downloads/test_data/net.kegg.txt")
## ------------------------------------------------------------------------
net.merged <-"http://research.scilifelab.se/andrej_alexeyenko/downloads/test_data/merged6_and_wir1_HC2"
net <- import.net(net.merged)
## ------------------------------------------------------------------------
data(net.kegg)
net <- import.net(net.kegg);
fgs.genes <- as_genes_fgs(net);
#save_gs_list(fgs.genes, File = "~/single_gene_ags.groups.tsv");
## ----include=TRUE--------------------------------------------------------
n1 <- nea.render(AGS=ags.list1, FGS=fgs.list, NET=net)
## ----fig.width=4, fig.height=4, fig.cap=c("n1$chi - chi-square estimate","n1$z- zscores", "NEA- pvalues","NEA-qvalues")----
hist(n1$chi, breaks=100)
hist(n1$z, breaks=100)
hist(n1$p, breaks=100)
hist(n1$q, breaks=100)
## ----include=T,fig.width=4, fig.height=3, fig.cap=c("g1$estimate - an estimate of the odds ratio", "g1$n - number of ags genes that belongs to corresponding fgs","g1$p - the p-value of the fishers.exact test","g1$q - Adjusted p-values by \"BH-method\"")----
ags.list2 <- samples2ags(fantom5.43samples, Ntop=1000, method="topnorm")
g1 <- gsea.render(AGS=ags.list2, FGS=fgs.list, Lowercase = 1,
ags.gene.col = 2, ags.group.col = 3, fgs.gene.col = 2, fgs.group.col = 3,
echo=1, Ntotal = 20000, Parallelize=1)
hist(log(g1$estimate), breaks=100)
hist(g1$n, breaks=100)
hist(g1$p, breaks=100)
hist(g1$q, breaks=100)
## ----include=T, results='hide', fig.cap=c("ROC curve evaluating KEGG network (net.kegg)\"")----
b0 <- benchmark (NET = net,
GS = fgs.list,
echo=1, graph=TRUE, na.replace = 0, mask = ".", minN = 0,
coff.z = 1.965, coff.fdr = 0.1, Parallelize=1);
## ----eval=FALSE----------------------------------------------------------
# b1 <- NULL;
# for (mask in c("kegg_", "go_")) {
# b1[[mask]] <- NULL;
# ref_list <- list(net.kegg=net.kegg,net.merged=net.merged)
# for (file.net in c("net.kegg","net.merged")) {
# # a series of networks can be put here: c("net.kegg1", "net.kegg2", "net.kegg3") in ref_list
# net <- import.net(ref_list[[file.net]], col.1 = 1, col.2 = 2, Lowercase = 1, echo = 1)
# b1[[mask]][[file.net]] <- benchmark (NET = net, GS = fgs.list, echo=1,
# graph=FALSE, na.replace = 0, mask = mask, minN = 0, Parallelize=3);
# roc(b1[["kegg_"]], coff.z = 2.57, main="kegg_");
# roc(b1[["go_"]], coff.z = 2.57, main="go_");
# }}
#
## ----include=FALSE-------------------------------------------------------
library(RColorBrewer)
library(MASS)
## ----results="hide", fig.cap=c("Node degree distribution"),fig.show='hold'----
connectivityfile <- system.file("extdata", "Connectivity.FC1_full", package = "NEArender")
connect <- connectivity(connectivityfile)
## ----include=T, results="hide", fig.cap=c("Second order topology"), fig.show='asis'----
topology2nd(NET=connectivityfile, Lowercase = 1, col.1 = 1, col.2 = 2)
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