YulongNiu

library('pheatmap')

##~~~~~~~~~~~~~~~~~~simulating data~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rn <- 100
cn <- 12
testdat <- matrix(rnorm(rn * cn), rn, cn)
testdat[1 : (rn/2), seq(1, cn, 2)] <- testdat[1 : (rn/2), seq(1, cn, 2)] + 5
testdat[(rn/2 + 1) : rn, seq(2, cn, 2)] <- testdat[(rn/2 + 1) : rn, seq(2, cn, 2)] + 7
testdat <- apply(testdat, 1:2, function(x) ifelse(x < 0, 0, x))

YulongNiu

#include <RcppArmadillo.h>
#include <RcppParallel.h>

#include <tthread/tinythread.h>
#include <algorithm>
#include <vector>

using namespace Rcpp;
using namespace RcppParallel;
using namespace arma;

YulongNiu

#include <RcppArmadillo.h>
#include <RcppParallel.h>

#include <algorithm>
#include <vector>

using namespace Rcpp;
using namespace RcppParallel;
using namespace arma;
using namespace std;

YulongNiu

#include <RcppArmadillo.h>
#include <RcppParallel.h>
#include <algorithm>
#include <cmath>

using namespace Rcpp;
using namespace RcppParallel;
using namespace arma;

// [[Rcpp::depends(RcppArmadillo, RcppParallel)]]

YulongNiu

library('microbenchmark')
library('Rcpp')
library('RcppParallel')
library('foreach')
library('parallel')
library('doParallel')
library('iterators')

sourceCpp('testrcpp.cpp')

YulongNiu

## set working path
setwd('/home/Yulong/RESEARCH/QAPTest/')

## to symmetric matrix
SymMat <- function(mat) {
  ## example
  ## tmp1 <- matrix(c(1, '-', '-', 2, 4, '-', 3, 5, 6), ncol = 3, byrow = TRUE)
  mat <- apply(mat, 1:2, as.character)
  mat <- ifelse(mat == '-', 0, mat)
  mat <- apply(mat, 1:2, as.numeric)

YulongNiu

#include <iostream>
#include <limits>

using namespace std;

int main() {

    int a = numeric_limits<int>::min();
    int b = numeric_limits<int>::max();

YulongNiu

#include <stdio.h>
#include <limits.h>
#include <float.h>

int main() {

    int a = INT_MIN;
    int b = INT_MAX;
    double c = DBL_MIN;

YulongNiu

#include <iostream>

int main() {
    double sum = 0.0;
    double step = 0.01;
    double each = 0.01;

    for (int i = 0; i < 100; ++i) {
        sum += step;
        step += each;

YulongNiu

###Download gff/fna/ptt/rnt annotation files of a prokaryotic genome ####

## Escherichia coli str. K-12 substr. MG1655 (E. coli)
## KEGG ID is 'eco' (http://www.genome.jp/kegg-bin/show_organism?org=eco)
## NCBI assembly ID is 'GCF_000005845.2' (https://www.ncbi.nlm.nih.gov/assembly/GCF_000005845.2)


library('ProGenome') ## version >= 0.06
library('magrittr')