README.md

In BioTIP: BioTIP: An R package for characterization of Biological Tipping-Point

BioTIP

An R package for biological tipping-point identification and characterization

Installation

You can install the newest version of BioTIP with:

library("devtools")
devtools::install_github("xyang2uchicago/BioTIP")

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:

```{r example} 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)) ```

enjoy!

BioTIP documentation built on Nov. 8, 2020, 6:27 p.m.