In TomKellyGenetics/slipt: Synthetic Lethal Interaction Prediction Tool (SLIPT) from Cancer Genomics Data

library("slipt")
if(!(require("multtest"))){
  source("http://bioconductor.org/biocLite.R")
  biocLite("multtest")
  library("multtest")
}

source("http://bioconductor.org/biocLite.R")
biocLite("multtest")
library("multtest")
data(golub)
rownames(golub) <- golub.gnames[,2]

plot(density(golub[1,]))
for(ii in 2:nrow(golub)) lines(density(golub[ii,]))

dim(golub)
golub.prep <- prep_data_for_SL(golub)
dim(golub.prep)
golub.prep[1:6, 1:6]

golub.SLtable <- detect_SL("WT1 Wilms tumor 1", golub.prep)
dim(golub.SLtable)
head(golub.SLtable[,c(11, 13, 15, 17)])

count_of_SL(golub.SLtable, significance = "raw")
head(table_of_SL(golub.SLtable, significance = "raw"))[,c(11, 13, 15, 17)]

golub.SLtable <- detect_SL("TP53 Tumor protein p53 (Li-Fraumeni syndrome)", golub.prep)
dim(golub.SLtable)
head(golub.SLtable[,c(11, 13, 15, 17)])

count_of_SL(golub.SLtable, significance = "raw")
count_of_SL(golub.SLtable, significance = "holm")
count_of_SL(golub.SLtable, significance = "fdr")
table_of_SL(golub.SLtable, significance = "fdr")[,c(11, 13, 15, 17)]

TomKellyGenetics/slipt documentation built on May 8, 2019, 9:28 a.m.