BioTIP

An R package for characterization of Biological Tipping-Point

Installation

You can install the released version of BioTIP from CRAN with:

install.packages("BioTIP")

or even better

source('http://bioconductor.org/biocLite.R')
biocLite("BioTIP")

Example

This is a basic example which shows you how to solve a common problem:

library(BioTIP)
data(GSE6136_matrix)
row.names(GSE6136_matrix) = GSE6136_matrix$ID_REF
GSE6136 = GSE6136_matrix[,-1]

data(GSE6136_cli)
cli = t(GSE6136_cli)

library(stringr)
colnames(cli) = str_split_fixed(cli[1,],'_',2)[,2]
cli = cli[-1,]
cli = data.frame(cli)
cli[,"cell-type:ch1"] = str_split_fixed(cli$characteristics_ch1.1,": ",2)[,2]
cli[,"Ig clonality:ch1"] = str_split_fixed(cli$characteristics_ch1.3,": ",2)[,2]

colnames(cli)[colnames(cli) == "cell-type:ch1"] = "group"
cli$Row.names = cli[,1]

df <- log2(dat+1)

tmp <- names(table(cli$group))
samplesL <- split(cli[,1],f = cli$group)
test <- sd_selection(df, samplesL,0.01)
igraphL <- getNetwork(test, fdr = 0.05)
cluster <- getCluster_methods(igraphL)
membersL_noweight <- getMCI(cluster,test,adjust.size = F)
plotBar_MCI(membersL_noweight,ylim = c(0,6))