The following steps are outlined to demonstrate the functionality of the Germ Line Age Calculator. These steps are to be used with the Illumina methylation array data sets (450k or EPIC). Specifically, the steps outlined below assume that beta-values (SWAN normalized) are available which can be performed with multiple different open source tools (ChAMP, Minfi, etc.) as well as other software tools (Partek).
Predicted ages are obtained via the call to a predict_germ_age() function.
The functoin expects the following arguments:
x- a numeric matrix of beta values.
X23 X28 X33 X47 X52 X34
0.13191 0.20154 0.107196 0.219992 0.109324 0.0830337
0.0394964 0.0288217 0.0502977 0.0289973 0.0499303 0.0345183
0.110789 0.0293556 0.0807749 0.0306088 0.0859292 0.0834235
0.0424816 0.0530358 0.0480805 0.0821266 0.0475171 0.0440236
0.106486 0.136325 0.0739211 0.114175 0.105706 0.109751
0.0468505 0.0410757 0.0406775 0.0277944 0.0375733 0.0484815
probeID- a vector of probe IDs for each row of thexmatrix.
"cg00050873" "cg00212031" "cg00213748" "cg00214611" "cg00455876" "cg01707559"
batch- sentrix barcode numbers for each column of thexmatrix.
1888849019, 1888849019, 1888849020, 1888849020, 1888849035, 1888849094
Main author:
Tim Jenkins (tim.jenkins@hsc.utah.edu)
Rewritten by:
Karolis Koncevičius (karolis.koncevicius@gmail.com)
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.