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comparison peakhelper.r @ 1:243f75d0ed6e draft default tip

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Uploaded. Includes new release 1.0.7 with fixed optional controls.
author messersc
date Thu, 19 Feb 2015 05:39:45 -0500
parents d42f4d78c85e
children
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0:d42f4d78c85e 1:243f75d0ed6e
1 ######################################################################################### 1 ########################################################################
2 #### Fixes output of peakfinder.r to produce proper narrowPeak format with proper scores 2 # JAMMv1.0.7rev1 is a peak finder for joint analysis of NGS replicates.
3 #### R script 3 # Copyright (C) 2014-2015 Mahmoud Ibrahim
4 ######################################################################################## 4 #
5 5 # This program is free software: you can redistribute it and/or modify
6 # it under the terms of the GNU General Public License as published by
7 # the Free Software Foundation, either version 3 of the License, or
8 # (at your option) any later version.
9 #
10 # This program is distributed in the hope that it will be useful,
11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 # GNU General Public License for more details.
14 #
15 # You should have received a copy of the GNU General Public License
16 # along with this program. If not, see <http://www.gnu.org/licenses/>.
17 #
18 # Contact: mahmoud.ibrahim@mdc-berlin.de
19 ########################################################################
6 20
7 21
8 22
9 # ======================= 23 # =======================
10 # User-defined variables 24 # User-defined variables
33 } 47 }
34 } 48 }
35 } 49 }
36 options(stringsAsFactors = FALSE) 50 options(stringsAsFactors = FALSE)
37 #=======================> DONE! 51 #=======================> DONE!
38
39
40
41
42 # ==============================================
43 # Required Libraries check (Source: http://r.789695.n4.nabble.com/test-if-a-package-is-installed-td1750671.htm)
44 # ==============================================
45 if ((is.element('sqldf', installed.packages()[,1]) == FALSE)) {
46 stop("R package 'sqldf' is required. Please install it!")
47 }
48 suppressPackageStartupMessages(library("sqldf"))
49 suppressPackageStartupMessages(library("tcltk"))
50 #=======================> DONE!
51
52 52
53 53
54 54
55 # ================= 55 # =================
56 # Custom Functions 56 # Custom Functions