lcolladotor

buildTileArray = function() {
    geomorphicTilesArray = new Array();
    var count = 0
    _.each(geomorphicTilesTableItems, function(geomorphicTilesTableItemsEach) {    
        obj = _.find(geomorphicTilesInformation, function(obj) {return obj.tileName == geomorphicTilesTableItemsEach.get("name");});
        if(obj.blocked == false){
            geomorphicTilesArray.push({
                tileName: geomorphicTilesTableItemsEach.get("name"),
                tileURL: geomorphicTilesTableItemsEach.get("avatar").replace("med.jpg?","thumb.jpg?"),
                edge: obj.edge,

lcolladotor

suppressPackageStartupMessages(library('rtracklayer'))

## Attempt with 1 file
bw <- BigWigFile('http://download.alleninstitute.org/brainspan/MRF_BigWig_Gencode_v10/bigwig/HSB97.AMY.bw')
seql <- seqlengths(bw)

## Then another file
bw2 <- BigWigFile('http://download.alleninstitute.org/brainspan/MRF_BigWig_Gencode_v10/bigwig/HSB114.A1C.bw')
seql2 <- seqlengths(bw2)

lcolladotor

> library('knitr')
> purl('derfinder.Rmd')


processing file: derfinder.Rmd
  |......                                                           |   9%Error in eval(expr, envir, enclos) : object 'windowsFlag' not found
  |.......                                                          |  11%Error in eval(expr, envir, enclos) : object 'windowsFlag' not found
  |.................................................................| 100%
output file: derfinder.R

lcolladotor

#' Change naming style for a set of sequence names
#'
#' If available, use the information from GenomeInfoDb for your species of 
#' interest to map the sequence names from the style currently used to another 
#' valid style. For example, for Homo sapiens map '2' (NCBI style) to 'chr2' 
#' (UCSC style). If the information from GenomeInfoDb is not available, the 
#' original sequence names will be returned.
#'
#' @param seqnames A character vector with the sequence names.
#' @param style A single character vector specifying the naming style to use

lcolladotor

--- /Users/lcollado/Desktop/env-Helen.txt	2014-11-03 23:34:56.000000000 -0500
+++ /Users/lcollado/Desktop/env-Leo.txt	2014-11-03 23:35:33.000000000 -0500
@@ -1,55 +1,62 @@
+$ env
 MANPATH=/jhpce/shared/community/core/perl/perl5/lib/perl5/man:/jhpce/shared/community/core/perl/perl5/share/man:/jhpce/shared/community/compiler/gcc/4.4.7/R/devel/share/man:/jhpce/shared/community/compiler/gcc/4.4.7/netcdf/4.3.2/share/man:/cm/shared/apps/sge/2011.11p1/man:/usr/local/share/man:/usr/share/man/overrides:/usr/share/man/en:/usr/share/man:/cm/local/apps/environment-modules/current/share/man
 _ModuleTable003_=LFsiZGVmYXVsdCJdPTEsWyJmdWxsTmFtZSJdPSJKSFBDRV90b29scy8xLjAiLFsibG9hZE9yZGVyIl09NCxwcm9wVD17fSxbInNob3J0Il09IkpIUENFX3Rvb2xzIixbInN0YXR1cyJdPSJhY3RpdmUiLH0sUj17WyJGTiJdPSIvamhwY2Uvc2hhcmVkL2NvbW11bml0eS9tb2R1bGVmaWxlcy9jb21waWxlci9nY2MvNC40LjcvUi9hbGwubHVhIixbImRlZmF1bHQiXT0xLFsiZnVsbE5hbWUiXT0iUi9hbGwiLFsibG9hZE9yZGVyIl09OCxwcm9wVD17fSxbInNob3J0Il09IlIiLFsic3RhdHVzIl09ImFjdGl2ZSIsfSxnY2M9e1siRk4iXT0iL2pocGNlL3NoYXJlZ

lcolladotor

library('derfinder')

## Set global species option
options(species = 'canis_familiaris')

## Load data
bam <- rep('10_130-chr11.bam', 6)
names(bam) <- paste0('Sample', 1:6)
fullCov <- fullCoverage(bam, chrs = c(1:38, 'X'))

lcolladotor

> library('derfinder')
>
> ## Set global species option
> options(species = 'canis_familiaris')
>
> ## Load data
> bam <- rep('10_130-chr11.bam', 6)
> names(bam) <- paste0('Sample', 1:6)
> fullCov <- fullCoverage(bam, chrs = c(1:38, 'X'))
2014-11-04 17:13:20 fullCoverage: processing chromosome 1

lcolladotor

---
output:
  knitrBootstrap::bootstrap_document:
    theme.chooser: TRUE
    highlight.chooser: TRUE
  html_document:
    toc: true
    theme: united
---

lcolladotor

   chr       mean        sd   n          se nChunks nCores nRound
1    1         NA        NA   0          NA     159     40      4
2    2 18.6456989 1.7351431  31 0.311640903     127     32      4
3    3  9.7551282 1.3304850  65 0.165026352     106     27      4
4    4  6.4531558 1.1958122 169 0.091985554      79     20      4
5    5 13.6833333 4.3116148  77 0.491354105      90     20      5
6    6 11.6014337 1.6933224  93 0.175589358      90     20      5
7    7 11.5335106 1.6975217  94 0.175085998      88     20      5
8    8  9.3085399 2.7116434 121 0.246513034      72     20      4
9    9 11.0740000 2.5358909 100 0.253589088      71     20      4

lcolladotor

#!/bin/bash
#$ -cwd
#$ -m e
#$ -l h=!compute-04[3-5]*

date