Mercurial > repos > messersc > jamm

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
0:d42f4d78c85e 1:243f75d0ed6e
1 ############################################################# 1 ########################################################################
2 #### Bin Size Calculator after Shimazaki and Shinomoto 2007 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 # 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 ########################################################################
5 20
6 21
7 # ======================= 22 # =======================
8 # User-defined variables 23 # User-defined variables
9 # ======================= 24 # =======================
169 frags = as.numeric(strsplit(frags, ",", fixed = TRUE)[[1]]) 184 frags = as.numeric(strsplit(frags, ",", fixed = TRUE)[[1]])
170 #=======================> DONE! 185 #=======================> DONE!
171 186
172 187
173 188
174 # ===================== 189 # ===================================================
175 # Shimazaki Procedure 190 # Shimazaki Procedure (Shimazaki and Shinomoto 2007)
176 # ===================== 191 # ===================================================
177 for (i in 1:length(ibed)) { 192 for (i in 1:length(ibed)) {
178 if (frags[i] > rl[i]) { 193 if (frags[i] > rl[i]) {
179 minbin = floor(frags[i] / 2) 194 minbin = floor(frags[i] / 2)
180 bins = c(bins, seq(minbin, minbin*15, by = minbin)) 195 bins = c(bins, seq(minbin, minbin*15, by = minbin))
181 } else { 196 } else {