In jmartinezot/findDE: Differentially Expressed Genes Discovery using ORdensity Method

# knitr options
knitr::opts_chunk$set(echo = TRUE)

# Install packages
# Load packages
# ...

library(knitr)

# Input / Output variables
# Tuning parameters
# ...
data <- "/home/bee/Github/ItziarParallelizing/WeTransfer/Datos_n20000.dat"

---

Test of ORdensity

Removing and installing

remove.packages('ORdensity')
install.packages("/home/bee/Github/ORdensity", repos = NULL, type = "source")
library('ORdensity')

Importing the file

a <- read.csv(data, sep=" ", header=TRUE)
x <- a[, 2:31]
y <- a[, 32:61]
positive <- as.matrix(x)
negative <- as.matrix(y)

Test with 1.000 (not parallel)

system.time(myORdensity <- new("ORdensity", Exp_cond_1 = positive, Exp_cond_2 = negative, parallel = FALSE, verbose = FALSE))

Test with 1.000 (parallel)

system.time(myORdensity <- new("ORdensity", Exp_cond_1 = positive, Exp_cond_2 = negative, parallel = TRUE, verbose = FALSE))

Summary

summary(myORdensity)

Median of medians

median_of_medians_of_distances <- function(v)
{
   d <- distances(v)
   l <- apply(d, 1, med)
   return (med(l))
}

jmartinezot/findDE documentation built on May 24, 2019, 8:54 a.m.