## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  warning = FALSE, 
  message = FALSE
)

set.seed(0)

## -----------------------------------------------------------------------------
phenof = system.file("extdata/", "example_phenotypes.txt", package = "diffdriver")
pheno <- read.table(phenof, header = T)
head(pheno)

## -----------------------------------------------------------------------------
genef = system.file("extdata", "example_gene.txt", package = "diffdriver")
gene <- read.table(genef, header = F)
head(gene)

## -----------------------------------------------------------------------------
mutf = system.file("extdata/", "example_mutations.txt", package = "diffdriver")
mut <- read.table(mutf, header = T)
head(mut)

## ----eval=FALSE---------------------------------------------------------------
# annodir = "/Volumes/Szhao/library/diffdriver_anno/annodir96"
# list.files(annodir)

## -----------------------------------------------------------------------------
# library(diffdriver)
set.seed(0)
output_dir <- "/tmp/diffdriver_output"

## ----eval=FALSE---------------------------------------------------------------
# library(diffdriver)
# res <- diffdriver(gene = gene, mut= mut, pheno = pheno, anno_dir = "/Volumes/Szhao/library/diffdriver_anno/annodir96", k=6, totalnttype = 96, BMRmode = "signature", output_dir = output_dir, output_prefix = "testdiffdriver_sig")
# res

## ----eval=FALSE---------------------------------------------------------------
# res <- diffdriver(gene = gene, mut= mut, pheno = pheno,  anno_dir = "/Volumes/Szhao/library/diffdriver_anno/annodir96", totalnttype = 96, BMRmode = "regular", output_dir = output_dir, output_prefix = "testdiffdriver_reg")
# res

## ----plot, eval=FALSE---------------------------------------------------------
# diffdriver::plot_mut(gene_name = "PIK3CA", mut= mut, pheno = pheno, totalnttype = 9, anno_dir = "/Volumes/Szhao/library/diffdriver_anno/annodir9")

## -----------------------------------------------------------------------------
sessionInfo()