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common.global.r
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common.global.r
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#####
# utils
old.repos <- getOption("repos")
on.exit(options(repos = old.repos))
new.repos <- old.repos
new.repos["CRAN"] <- "http://cran.stat.ucla.edu"
options(repos = new.repos)
source("http://www.bioconductor.org/biocLite.R")
#if(!suppressMessages(require("BiocInstaller",quietly=T))){
# install.packages("BiocInstaller", repos="http://www.bioconductor.org/packages/2.13/bioc")
#}
ris <- function(x){if(!require(x,character.only=T,quietly=T,warn.conflicts=F)){
install.packages(x)
require(x,character.only=T,quietly=T,warn.conflicts=F)
}}
bis <- function(x){if(!require(x,character.only=T,quietly=T,warn.conflicts=F)){
biocLite(x)
require(x,character.only=T,quietly=T,warn.conflicts=F)
}}
wipetemp <- function(){
x <- readline("this will wipe existing temp files (y/n)")
if(x=="y"){
print("wiping temp")
unlink("tmp/*")
}else{
print("keeping temp")
}
}
set.seed(1)
####
# dependencies
suppressMessages(require('BiocInstaller',quietly=T))
suppressMessages(bis("Rsamtools"))
suppressMessages(bis("GenomicAlignments"))
suppressMessages(bis('Biostrings'))
suppressMessages(bis('seqLogo'))
suppressMessages(ris('RSofia'))
suppressMessages(ris('statmod'))
suppressMessages(ris('Rcpp'))
suppressMessages(ris('inline'))
suppressMessages(require(Matrix,quietly=T))
####
# params
#window size
wsize = 300
#fast mode
fast.mode = T
#seqbias mode
avoid.seqbias = F