dakl

# This function takes A and M-values (or any X and Y )
lowessNormalization <- function(x, y, include = TRUE, line = NULL, 
         ...) {
         isFinite <- (is.finite(x) & is.finite(y))
         if (any(isFinite)){
             if (is.null(line)) {
                 line <- lowess(x[isFinite & include], y[isFinite & 
                     include], ...)
             }
             y[isFinite] <- y[isFinite] - approx(line, xout = x[isFinite], 

dakl

lowessNormalization <- function(x, y, include = TRUE, line = NULL, 
         ...) {
         isFinite <- (is.finite(x) & is.finite(y))
         if (any(isFinite)){
             if (is.null(line)) {
                 line <- lowess(x[isFinite & include], y[isFinite & 
                     include], ...)
             }
             y[isFinite] <- y[isFinite] - approx(line, xout = x[isFinite], 
                 ties = mean)$y

dakl

lowessNormalization <- function(x, y, include = TRUE, line = NULL, 
         ...) {
         isFinite <- (is.finite(x) & is.finite(y))
         if (any(isFinite)){
             if (is.null(line)) {
                 line <- lowess(x[isFinite & include], y[isFinite & 
                     include], ...)
             }
             y[isFinite] <- y[isFinite] - approx(line, xout = x[isFinite], 
                 ties = mean)$y

dakl

# filter flags
ff <- function(f, flags){
  ## if !all(dim(mat) == dim(flags)) break say "data and flags must have identical dimensions"
  for(k in 1:ncol(f)){
    idx.flags <- which( flags[,k] < 0 )
    f[idx.flags,k] <- NA
    cat("Number features filtered on slide ", k, ": ", length(idx.flags), "\n", sep="")
  }
  f
}

dakl

#!/usr/bin/env bash
# memusg -- Measure memory usage of processes
# Usage: memusg COMMAND [ARGS]...
#
# Author: Jaeho Shin <[email protected]>
# Created: 2010-08-16
set -um

# check input
[ $# -gt 0 ] || { sed -n '2,/^#$/ s/^# //p' <"$0"; exit 1; }

dakl

From 5f60239292d8d963997aeb14201e2e9eb2635c63 Mon Sep 17 00:00:00 2001
From: Daniel Klevebring <[email protected]>
Date: Wed, 24 Sep 2014 06:42:15 +0000
Subject: [PATCH] added quotes around  to build on centos 6.5

---
 Analysis/CMakeLists.txt                      |    2 +-
 buildTools/cmake/CMakeLists.compiler.txt     |    4 ++--
 buildTools/cmake/CMakeLists.dependencies.txt |   26 +++++++++++++-------------
 buildTools/cmake/CMakeLists.version.txt      |    6 +++---

dakl

circle <- function(x, y, r, ...) {
    ang <- seq(0, 2*pi, length = 100)
    xx <- x + r * cos(ang)
    yy <- y + r * sin(ang)
    polygon(xx, yy, ...)
}

venndia <- function(A, B, C, alab="A", blab="B", clab="C", getdata=FALSE, cex.text=2, cex.num=2, plot=TRUE, xlim=c(0,9), ylim=c(0,9), ...){
	cMissing <- missing(C)
	if(cMissing){ C <- c() }

dakl

$ brew install sailfish -v 
tbb: OS X Lion or newer is required.
==> Downloading https://github.com/kingsfordgroup/sailfish/releases/download/v0.6.2/Sailfish-0.6.2-Source.tar.gz
Already downloaded: /home/kleve/.cache/Homebrew/sailfish-0.6.2.tar.gz
==> Verifying sailfish-0.6.2.tar.gz checksum
tar xf /home/kleve/.cache/Homebrew/sailfish-0.6.2.tar.gz
==> cmake .. -DCMAKE_INSTALL_PREFIX=/gulo/glob/kleve/private/linuxbrew/Cellar/sailfish/0.6.2 -DCMAKE_BUILD_TYPE=None -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_VERBOSE_MAKEFILE=ON -Wno-dev
-- The C compiler identification is GNU 4.9.1
-- The CXX compiler identification is GNU 4.9.1
-- Check for working C compiler: /gulo/glob/kleve/private/linuxbrew/bin/gcc-4.9

dakl

# This function sorts the matrix for better visualization of mutual exclusivity across genes
memoSort <- function(M) {
	geneOrder <- sort(rowSums(M), decreasing=TRUE, index.return=TRUE)$ix;
	scoreCol <- function(x) {
		score <- 0;
		for(i in 1:length(x)) {
			if(x[i]) {
				score <- score + 2^(length(x)-i);
			}
		}

dakl

@HD     VN:1.4  SO:coordinate
@SQ     SN:chrM LN:16571
@SQ     SN:chr1 LN:249250621
@SQ     SN:chr2 LN:243199373
@SQ     SN:chr3 LN:198022430
@SQ     SN:chr4 LN:191154276
@SQ     SN:chr5 LN:180915260
@SQ     SN:chr6 LN:171115067
@SQ     SN:chr7 LN:159138663
@SQ     SN:chr8 LN:146364022