An R package for biological tipping-point identification and characterization
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")
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)) ```
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