lytze

groups <- c("Group", "Names") # here are the group names for enrichment experiments, also folder names locates homer motif files
p_threash <- 1e-4 # p-value threashold

## make separate meme file for each homer file
for (g in groups) {
    homer <- readLines(paste0("../data/homer_motifs/", g, "/homerMotifs.all.motifs"))
    homer_starts <- grep("^>", homer)
    homer_number <- length(homer_starts)
    homer_lines <- length(homer)
    homer_starts[homer_number + 1] <- homer_lines + 1

lytze

library(shiny)
library(datasets)
Logged = FALSE;
PASSWORD <- data.frame(Brukernavn = "withr", Passord = "25d55ad283aa400af464c76d713c07ad")
# Define server logic required to summarize and view the selected dataset
shinyServer(function(input, output) {
  source("www/Login.R",  local = TRUE)
  
  observe({
    if (USER$Logged == TRUE) {

lytze

#!/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_3.0.2/bin/Rscript

# Eric Vallabh Minikel
# CureFFI.org
# 2014-01-14
# example of how to use optparse in R scripts

# usage: ./exampleRScript1.r -a thisisa -b hiagain
#        ./exampleRScript1.r --avar thisisa --bvar hiagain

lytze

#! /usr/bin/Rscript
# Lytze Nov 4 2014
# An example of visit stdin (the real stdin, not the console) using RScript
# NO details about seting opts and args

# Usage:
## $ chmod u+x find_k_mer.R
## $ ./find_k_mer.R
# OR
## $ ./find_k_mer.R < inputfile

lytze

doInstall <- TRUE  # Change to FALSE if you don't want packages installed.
toInstall <- c("ReadImages", "reshape", "ggplot2")
if(doInstall){install.packages(toInstall, repos = "http://cran.r-project.org")}
lapply(toInstall, library, character.only = TRUE)

imageLoader <- function(url){  # This function takes a URL, and generates a data.frame with pixel locations and colors
  # Download to disk, load
  download.file(url, "tempPicture.jpg", mode = "wb")  # Stash image locally
  readImage <- read.jpeg("tempPicture.jpg")