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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methylkit commit 14f0b39f64982773ef0367379b915f742eabcc1b |
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methylkit.xml test-data/input_control1.myCpG.txt test-data/input_control2.myCpG.txt test-data/input_test1.myCpG.txt test-data/input_test2.myCpG.txt test-data/output_MethPerChr.tsv test-data/output_MethylDiff.bedgraph test-data/output_PCA.pdf test-data/output_clustering.pdf test-data/output_correlation.pdf test-data/output_myDiff.bedgraph test-data/output_seg_diff.bed test-data/output_seg_raw.bed test-data/output_statistics.pdf test-data/test.r |
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| diff -r 000000000000 -r a8705df7c57f methylkit.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/methylkit.xml Wed Dec 21 17:30:57 2016 -0500 |
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| b'@@ -0,0 +1,527 @@\n+<tool id="methylkit" name="methylKit" version="0.99.2">\n+ <description>DNA methylation analysis and annotation</description>\n+ <macros>\n+ <macro name="differential_methylation">\n+ <param name="overdispersion" type="select"\n+ label="overdispersion"\n+ help="if set to \'none\' (default), no overdispersion\n+ correction will be attempted. \'MN\' applies a scaling\n+ parameter to variance estimated by the model.\n+ If set to \'shrinkMN\' (experimental parameter),\n+ scaling parameter will be shrunk towards a common value">\n+ <option value="none" selected="True">\n+ none\n+ </option>\n+ <option value="MN">\n+ MN\n+ </option>\n+ <option value="shrinkMN">\n+ shrinkMN\n+ </option>\n+ </param>\n+ <param name="adjust" type="select"\n+ label="adjust"\n+ help="different methods to correct the p-values\n+ for multiple testing (default: SLIM).">\n+ <option value="SLIM" selected="True">\n+ SLIM\n+ </option>\n+ <option value="holm">\n+ holm\n+ </option>\n+ <option value="hochberg">\n+ hochberg\n+ </option>\n+ <option value="hommel">\n+ hommel\n+ </option>\n+ <option value="bonferroni">\n+ bonferroni\n+ </option>\n+ <option value="BH">\n+ BH\n+ </option>\n+ <option value="BY">\n+ BY\n+ </option>\n+ <option value="fdr">\n+ fdr\n+ </option>\n+ <option value="none">\n+ none\n+ </option>\n+ <option value="qvalue">\n+ qvalue\n+ </option>\n+ </param>\n+ <param name="effect" type="select"\n+ label="effect"\n+ help="method to calculate the mean methylation different\n+ between groups using read coverage as weights (default: wmean).\n+ When set to \'mean\', the generic mean is applied and when\n+ set to \'predicted\', predicted means from the logistic\n+ regression model is used for calculating the effect.">\n+ <option value="wmean" selected="True">\n+ wmean\n+ </option>\n+ <option value="mean">\n+ mean\n+ </option>\n+ <option value="predicted">\n+ predicted\n+ </option>\n+ </param>\n+ <param name="test" type="select"\n+ label="test"\n+ help="the statistical test used to determine\n+ the methylation differences (default: Chisq-test).\n+ The F-test can be chosen\n+ if overdispersion control is applied.">\n+ <option value="Chisq" selected="True">\n+ Chisq\n+ </option>\n+ <option value="F">\n+ F\n+ </option>\n+ </param>\n+ <param name="qvalue_cutoff" type="float"\n+ value="0.01" label="qvalue.cutoff"\n+ help="cutoff for qvalue of differential methylation statistic (default:0.01)">\n+ <validator type="in_range"\n+ message="Minimum 0 and maximum 1" min="0" max="1"/>\n+ </param>\n+ <param name="meth_cutoff" type="float"\n+ value="25" label="meth.cutoff"\n+ help="cutoff for absolute value of methylation percentage change between test and control (default:25)">\n+ <validator type="in_range"\n+ message="Minimum 0 and maximum 100" min="0" max="100"/>\n+ </param>\n+ <param name="type" type="selec'..b'>\n+ <param name="overdispersion" value="none" />\n+ <param name="adjust" value="SLIM" />\n+ <param name="effect" value="wmean" />\n+ <param name="test" value="Chisq" />\n+ <param name="qvalue_cutoff" value="0.01" />\n+ <param name="meth_cutoff" value="25" />\n+ <param name="type" value="all" />\n+ <param name="dist" value="correlation" />\n+ <param name="method" value="ward" />\n+ <output name="output_statistics" file="output_statistics.pdf"\n+ ftype="pdf" compare="sim_size"/>\n+ <output name="output_correlation" file="output_correlation.pdf"\n+ ftype="pdf" compare="sim_size"/>\n+ <output name="output_myDiff" file="output_myDiff.bedgraph"\n+ ftype="bedgraph"/>\n+ <output name="output_MethPerChr" file="output_MethPerChr.tsv"\n+ ftype="tabular"/>\n+ <output name="output_MethylDiff" file="output_MethylDiff.bedgraph"\n+ ftype="bedgraph"/>\n+ <output name="output_clustering" file="output_clustering.pdf"\n+ ftype="pdf" compare="sim_size"/>\n+ <output name="output_PCA" file="output_PCA.pdf"\n+ ftype="pdf" compare="sim_size"/>\n+ <output name="output_seg_raw" file="output_seg_raw.bed"\n+ ftype="bed"/>\n+ <output name="output_seg_diff" file="output_seg_diff.bed"\n+ ftype="bed"/>\n+ </test>\n+ </tests>\n+<help>\n+<![CDATA[\n+.. class:: infomark\n+\n+**What it does**\n+\n+`methylKit`_ is an R package for DNA methylation analysis and annotation\n+from high-throughput bisulfite sequencing.\n+The package is designed to deal with sequencing data from RRBS and\n+its variants, but also target-capture methods such as Agilent SureSelect\n+methyl-seq. In addition, methylKit can deal with base-pair resolution data\n+for 5hmC obtained from Tab-seq or oxBS-seq. It can also handle whole-genome\n+bisulfite sequencing data if proper input format is provided.\n+\n+.. _methylKit: https://github.com/al2na/methylKit\n+\n+The Galaxy tool enables three types of analysis:\n+ * differential methylation\n+ * clustering\n+ * segmentation\n+\n+The user can choose to run all provided analysis or run an individual one.\n+\n+.. class:: infomark\n+\n+**Input**\n+\n+Typically, bisulfite converted reads are aligned to the genome and %\n+methylation value per base is calculated by processing alignments.\n+methylKit takes that % methylation value per base information as input.\n+Such input file may be obtained from `AMP`_ pipeline\n+for aligning RRBS reads. A typical input file looks like this::\n+\n+\n+ chrBase chr base strand coverage freqC freqT\n+\n+ chr21.9764539 chr21 9764539 R 12 25.00 75.00\n+\n+ chr21.9764513 chr21 9764513 F 12 0.00 100.00\n+\n+\n+.. _AMP: http://code.google.com/p/amp-errbs/\n+\n+.. class:: infomark\n+\n+**Output**\n+\n+The outputs from differential methylation\n+ * ``differential methylation``: The `bedgraph`_ file contains differentially methylated bases/regions and the corresponding statistics.\n+ * ``differential methylation - subset``: The bedgraph file contains the subset of differentially methylated bases/regions that satisfies the user defined thresholds with qvalue.cutoff and meth.cutoff.\n+ * ``number of hyper/hypo sites``: The tabular file contains number of hyper/hypo methylated regions/bases.\n+\n+.. _bedgraph: https://genome.ucsc.edu/goldenpath/help/bedgraph.html\n+\n+The outputs from clustering\n+ * ``hierarchical clustering``: The figure shows hierarchical clustering using methylation data.\n+ * ``PCA``: The figure shows principal components analysis of methylation data.\n+\n+The output from segmentation\n+ * ``methylation segment``: The `bed`_ file contains the profile of methylation segment.\n+ * ``differential methylation segment``: The bed file contains the profile of differential methylation segment.\n+\n+.. _bed: https://genome.ucsc.edu/FAQ/FAQformat#format1\n+]]>\n+</help>\n+<citations>\n+ <citation type="doi">10.1186/gb-2012-13-10-r87</citation>\n+</citations>\n+</tool>\n' |
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| diff -r 000000000000 -r a8705df7c57f test-data/input_control1.myCpG.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_control1.myCpG.txt Wed Dec 21 17:30:57 2016 -0500 |
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| b'@@ -0,0 +1,2378 @@\n+chrBase\tchr\tbase\tstrand\tcoverage\tfreqC\tfreqT\n+chr21.9826907\tchr21\t9826907\tF\t96\t18.75\t81.25\n+chr21.9853326\tchr21\t9853326\tF\t16\t87.50\t12.50\n+chr21.9853296\tchr21\t9853296\tF\t18\t88.89\t11.11\n+chr21.9860126\tchr21\t9860126\tF\t83\t100.00\t0.00\n+chr21.9906663\tchr21\t9906663\tR\t14\t92.86\t7.14\n+chr21.9906677\tchr21\t9906677\tR\t14\t78.57\t21.43\n+chr21.9906700\tchr21\t9906700\tF\t30\t26.67\t73.33\n+chr21.9906954\tchr21\t9906954\tF\t30\t86.67\t13.33\n+chr21.9906644\tchr21\t9906644\tF\t23\t95.65\t4.35\n+chr21.9906873\tchr21\t9906873\tF\t15\t26.67\t73.33\n+chr21.9906634\tchr21\t9906634\tF\t23\t69.57\t30.43\n+chr21.9906704\tchr21\t9906704\tF\t18\t94.44\t5.56\n+chr21.9906655\tchr21\t9906655\tR\t14\t92.86\t7.14\n+chr21.9906645\tchr21\t9906645\tR\t13\t100.00\t0.00\n+chr21.9906926\tchr21\t9906926\tR\t17\t64.71\t35.29\n+chr21.9906619\tchr21\t9906619\tF\t22\t81.82\t18.18\n+chr21.9906949\tchr21\t9906949\tF\t30\t53.33\t46.67\n+chr21.9906910\tchr21\t9906910\tR\t16\t56.25\t43.75\n+chr21.9906907\tchr21\t9906907\tR\t17\t11.76\t88.24\n+chr21.9906681\tchr21\t9906681\tF\t37\t37.84\t62.16\n+chr21.9906955\tchr21\t9906955\tR\t13\t69.23\t30.77\n+chr21.9906724\tchr21\t9906724\tF\t18\t72.22\t27.78\n+chr21.9906822\tchr21\t9906822\tR\t14\t100.00\t0.00\n+chr21.9906808\tchr21\t9906808\tR\t13\t100.00\t0.00\n+chr21.9906847\tchr21\t9906847\tR\t14\t71.43\t28.57\n+chr21.9906660\tchr21\t9906660\tR\t14\t64.29\t35.71\n+chr21.9906839\tchr21\t9906839\tR\t13\t69.23\t30.77\n+chr21.9906846\tchr21\t9906846\tF\t15\t93.33\t6.67\n+chr21.9906928\tchr21\t9906928\tR\t17\t64.71\t35.29\n+chr21.9906657\tchr21\t9906657\tR\t14\t0.00\t100.00\n+chr21.9906641\tchr21\t9906641\tR\t14\t0.00\t100.00\n+chr21.9906676\tchr21\t9906676\tF\t39\t100.00\t0.00\n+chr21.9906934\tchr21\t9906934\tR\t17\t100.00\t0.00\n+chr21.9906890\tchr21\t9906890\tR\t17\t0.00\t100.00\n+chr21.9906884\tchr21\t9906884\tF\t13\t15.38\t84.62\n+chr21.9906841\tchr21\t9906841\tR\t14\t71.43\t28.57\n+chr21.9906864\tchr21\t9906864\tF\t14\t71.43\t28.57\n+chr21.9906714\tchr21\t9906714\tF\t25\t76.00\t24.00\n+chr21.9906824\tchr21\t9906824\tR\t14\t100.00\t0.00\n+chr21.9906635\tchr21\t9906635\tR\t13\t53.85\t46.15\n+chr21.9906952\tchr21\t9906952\tF\t30\t83.33\t16.67\n+chr21.9906640\tchr21\t9906640\tF\t23\t0.00\t100.00\n+chr21.9906957\tchr21\t9906957\tF\t30\t86.67\t13.33\n+chr21.9906604\tchr21\t9906604\tF\t23\t78.26\t21.74\n+chr21.9906992\tchr21\t9906992\tR\t13\t92.31\t7.69\n+chr21.9906950\tchr21\t9906950\tR\t13\t61.54\t38.46\n+chr21.9906902\tchr21\t9906902\tR\t17\t0.00\t100.00\n+chr21.9906805\tchr21\t9906805\tR\t13\t61.54\t38.46\n+chr21.9906889\tchr21\t9906889\tF\t12\t0.00\t100.00\n+chr21.9906933\tchr21\t9906933\tF\t29\t89.66\t10.34\n+chr21.9906694\tchr21\t9906694\tF\t39\t41.03\t58.97\n+chr21.9906885\tchr21\t9906885\tR\t16\t0.00\t100.00\n+chr21.9906869\tchr21\t9906869\tF\t15\t0.00\t100.00\n+chr21.9906958\tchr21\t9906958\tR\t13\t100.00\t0.00\n+chr21.9906616\tchr21\t9906616\tF\t23\t60.87\t39.13\n+chr21.9906931\tchr21\t9906931\tR\t17\t35.29\t64.71\n+chr21.9906827\tchr21\t9906827\tR\t14\t35.71\t64.29\n+chr21.9906953\tchr21\t9906953\tR\t13\t84.62\t15.38\n+chr21.9911447\tchr21\t9911447\tR\t10\t100.00\t0.00\n+chr21.9911433\tchr21\t9911433\tR\t10\t90.00\t10.00\n+chr21.9911345\tchr21\t9911345\tF\t10\t90.00\t10.00\n+chr21.9913543\tchr21\t9913543\tF\t34\t91.18\t8.82\n+chr21.9913575\tchr21\t9913575\tF\t33\t93.94\t6.06\n+chr21.9917414\tchr21\t9917414\tR\t11\t100.00\t0.00\n+chr21.9917398\tchr21\t9917398\tR\t11\t90.91\t9.09\n+chr21.9917607\tchr21\t9917607\tF\t49\t77.55\t22.45\n+chr21.9917608\tchr21\t9917608\tR\t12\t75.00\t25.00\n+chr21.9917582\tchr21\t9917582\tF\t61\t85.25\t14.75\n+chr21.9917587\tchr21\t9917587\tF\t59\t77.97\t22.03\n+chr21.9917630\tchr21\t9917630\tR\t14\t85.71\t14.29\n+chr21.9917629\tchr21\t9917629\tF\t28\t0.00\t100.00\n+chr21.9927676\tchr21\t9927676\tR\t18\t100.00\t0.00\n+chr21.9927687\tchr21\t9927687\tR\t18\t100.00\t0.00\n+chr21.9927527\tchr21\t9927527\tF\t32\t100.00\t0.00\n+chr21.9944663\tchr21\t9944663\tR\t45\t77.78\t22.22\n+chr21.9944505\tchr21\t9944505\tF\t86\t91.86\t8.14\n+chr21.9959569\tchr21\t9959569\tR\t40\t100.00\t0.00\n+chr21.9959577\tchr21\t9959577\tR\t40\t100.00\t0.00\n+chr21.9959644\tchr21\t9959644\tR\t59\t88.14\t11.86\n+chr21.9959541\tchr21\t9959541\tR\t39\t94.87\t5.13\n+chr21.9959407\tchr21\t9959407\tF\t52\t94.23\t5.77\n+chr21.9959650\tchr21\t9959650\tR\t59\t86.44\t13.56\n+chr21.9967634\tchr21\t9967634\tR\t93\t66.67\t33.33\n+chr21.9990967\tchr21\t9990967\tF\t16\t81.25\t18.75\n+chr21.10011861\tchr21\t10011861\tF\t39\t33.33\t66.67\n+chr21.10012079\tchr21\t10012079\tF\t7'..b'chr21\t18576211\tR\t12\t100.00\t0.00\n+chr21.18578901\tchr21\t18578901\tF\t13\t100.00\t0.00\n+chr21.18578884\tchr21\t18578884\tF\t13\t100.00\t0.00\n+chr21.18582975\tchr21\t18582975\tF\t23\t86.96\t13.04\n+chr21.18582970\tchr21\t18582970\tF\t23\t100.00\t0.00\n+chr21.18615698\tchr21\t18615698\tR\t26\t100.00\t0.00\n+chr21.18713648\tchr21\t18713648\tF\t24\t100.00\t0.00\n+chr21.18713624\tchr21\t18713624\tF\t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|
| b |
| diff -r 000000000000 -r a8705df7c57f test-data/input_control2.myCpG.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_control2.myCpG.txt Wed Dec 21 17:30:57 2016 -0500 |
| b |
| b'@@ -0,0 +1,1698 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|
| b |
| diff -r 000000000000 -r a8705df7c57f test-data/input_test1.myCpG.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_test1.myCpG.txt Wed Dec 21 17:30:57 2016 -0500 |
| b |
| b'@@ -0,0 +1,1905 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21.18539344\tchr21\t18539344\tF\t18\t16.67\t83.33\n+chr21.18539277\tchr21\t18539277\tR\t72\t4.17\t95.83\n+chr21.18539048\tchr21\t18539048\tR\t61\t26.23\t73.77\n+chr21.18539218\tchr21\t18539218\tR\t79\t46.84\t53.16\n+chr21.18539222\tchr21\t18539222\tR\t80\t35.00\t65.00\n+chr21.18539240\tchr21\t18539240\tR\t77\t18.18\t81.82\n+chr21.18539148\tchr21\t18539148\tF\t25\t0.00\t100.00\n+chr21.18538816\tchr21\t18538816\tF\t12\t8.33\t91.67\n+chr21.18539231\tchr21\t18539231\tR\t79\t48.10\t51.90\n+chr21.18539613\tchr21\t18539613\tR\t10\t0.00\t100.00\n+chr21.18539545\tchr21\t18539545\tR\t10\t0.00\t100.00\n+chr21.18539117\tchr21\t18539117\tF\t25\t0.00\t100.00\n+chr21.18539208\tchr21\t18539208\tR\t75\t60.00\t40.00\n+chr21.18539805\tchr21\t18539805\tR\t21\t0.00\t100.00\n+chr21.18539259\tchr21\t18539259\tF\t90\t21.11\t78.89\n+chr21.18539297\tchr21\t18539297\tF\t27\t7.41\t92.59\n+chr21.18539053\tchr21\t18539053\tR\t62\t17.74\t82.26\n+chr21.18539009\tchr21\t18539009\tF\t147\t12.93\t87.07\n+chr21.18539585\tchr21\t18539585\tR\t10\t0.00\t100.00\n+chr21.18539264\tchr21\t18539264\tF\t94\t23.40\t76.60\n+chr21.18539622\tchr21\t18539622\tF\t16\t0.00\t100.00\n+chr21.18539016\tchr21\t18539016\tF\t140\t22.14\t77.86\n+chr21.18539346\tchr21\t18539346\tF\t16\t0.00\t100.00\n+chr21.18550887\tchr21\t18550887\tF\t15\t53.33\t46.67\n+chr21.18572834\tchr21\t18572834\tF\t10\t80.00\t20.00\n+chr21.18572866\tchr21\t18572866\tF\t10\t100.00\t0.00\n+chr21.18576203\tchr21\t18576203\tR\t11\t45.45\t54.55\n+chr21.18576157\tchr21\t18576157\tF\t14\t100.00\t0.00\n+chr21.18576145\tchr21\t18576145\tF\t14\t85.71\t14.29\n+chr21.18576141\tchr21\t18576141\tF\t15\t100.00\t0.00\n+chr21.18576179\tchr21\t18576179\tR\t11\t100.00\t0.00\n+chr21.18576178\tchr21\t18576178\tF\t11\t100.00\t0.00\n+chr21.18576211\tchr21\t18576211\tR\t11\t100.00\t0.00\n+chr21.18582975\tchr21\t18582975\tF\t18\t61.11\t38.89\n+chr21.18582970\tchr21\t18582970\tF\t18\t66.67\t33.33\n+chr21.18615698\tchr21\t18615698\tR\t24\t66.67\t33.33\n+chr21.18713648\tchr21\t18713648\tF\t12\t66.67\t33.33\n+chr21.18713624\tchr21\t18713624\tF\t12\t91.67\t8.33\n+chr21.18713634\tchr21\t18713634\tF\t12\t100.00\t0.00\n+chr21.18737675\tchr21\t18737675\tF\t12\t58.33\t41.67\n+chr21.18737730\tchr21\t18737730\tR\t13\t61.54\t38.46\n+chr21.18763228\tchr21\t18763228\tF\t11\t0.00\t100.00\n+chr21.18763284\tchr21\t18763284\tR\t10\t0.00\t100.00\n+chr21.18957876\tchr21\t18957876\tF\t16\t56.25\t43.75\n+chr21.19280741\tchr21\t19280741\tF\t10\t80.00\t20.00\n+chr21.19282009\tchr21\t19282009\tF\t11\t100.00\t0.00\n+chr21.19390694\tchr21\t19390694\tR\t14\t64.29\t35.71\n+chr21.19390691\tchr21\t19390691\tR\t14\t57.14\t42.86\n+chr21.19422671\tchr21\t19422671\tR\t17\t88.24\t11.76\n+chr21.19539486\tchr21\t19539486\tR\t10\t70.00\t30.00\n+chr21.19539511\tchr21\t19539511\tR\t12\t66.67\t33.33\n+chr21.19539528\tchr21\t19539528\tR\t12\t100.00\t0.00\n+chr21.19579361\tchr21\t19579361\tR\t12\t83.33\t16.67\n+chr21.19579345\tchr21\t19579345\tR\t10\t80.00\t20.00\n+chr21.19579352\tchr21\t19579352\tR\t12\t50.00\t50.00\n+chr21.19579357\tchr21\t19579357\tR\t12\t83.33\t16.67\n+chr21.19579289\tchr21\t19579289\tF\t23\t43.48\t56.52\n+chr21.19626227\tchr21\t19626227\tR\t25\t88.00\t12.00\n+chr21.19626384\tchr21\t19626384\tR\t22\t100.00\t0.00\n+chr21.19711774\tchr21\t19711774\tF\t10\t20.00\t80.00\n+chr21.19739452\tchr21\t19739452\tF\t10\t90.00\t10.00\n+chr21.19788122\tchr21\t19788122\tR\t46\t93.48\t6.52\n+chr21.19788113\tchr21\t19788113\tR\t46\t100.00\t0.00\n+chr21.19788089\tchr21\t19788089\tR\t45\t100.00\t0.00\n+chr21.19788073\tchr21\t19788073\tR\t45\t93.33\t6.67\n+chr21.19788076\tchr21\t19788076\tR\t44\t95.45\t4.55\n+chr21.19788117\tchr21\t19788117\tR\t46\t100.00\t0.00\n+chr21.19788093\tchr21\t19788093\tR\t45\t100.00\t0.00\n+chr21.19834041\tchr21\t19834041\tF\t10\t100.00\t0.00\n+chr21.19834070\tchr21\t19834070\tF\t10\t30.00\t70.00\n+chr21.19855690\tchr21\t19855690\tF\t27\t96.30\t3.70\n+chr21.19855659\tchr21\t19855659\tF\t10\t100.00\t0.00\n+chr21.19855711\tchr21\t19855711\tF\t18\t100.00\t0.00\n+chr21.19855706\tchr21\t19855706\tF\t27\t100.00\t0.00\n+chr21.19943653\tchr21\t19943653\tF\t12\t100.00\t0.00\n+chr21.19943695\tchr21\t19943695\tF\t12\t91.67\t8.33\n' |
| b |
| diff -r 000000000000 -r a8705df7c57f test-data/input_test2.myCpG.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_test2.myCpG.txt Wed Dec 21 17:30:57 2016 -0500 |
| b |
| b'@@ -0,0 +1,2007 @@\n+chrBase\tchr\tbase\tstrand\tcoverage\tfreqC\tfreqT\n+chr21.9764513\tchr21\t9764513\tR\t20\t75.00\t25.00\n+chr21.9764539\tchr21\t9764539\tR\t20\t95.00\t5.00\n+chr21.9767701\tchr21\t9767701\tF\t10\t10.00\t90.00\n+chr21.9804584\tchr21\t9804584\tF\t10\t90.00\t10.00\n+chr21.9804595\tchr21\t9804595\tF\t10\t100.00\t0.00\n+chr21.9802620\tchr21\t9802620\tF\t13\t61.54\t38.46\n+chr21.9802590\tchr21\t9802590\tF\t13\t76.92\t23.08\n+chr21.9809998\tchr21\t9809998\tF\t150\t85.33\t14.67\n+chr21.9809957\tchr21\t9809957\tF\t15\t20.00\t80.00\n+chr21.9796127\tchr21\t9796127\tF\t10\t100.00\t0.00\n+chr21.9809695\tchr21\t9809695\tF\t12\t91.67\t8.33\n+chr21.9797216\tchr21\t9797216\tF\t13\t38.46\t61.54\n+chr21.9809684\tchr21\t9809684\tF\t12\t83.33\t16.67\n+chr21.9797212\tchr21\t9797212\tF\t21\t71.43\t28.57\n+chr21.9799590\tchr21\t9799590\tF\t12\t58.33\t41.67\n+chr21.9797182\tchr21\t9797182\tF\t23\t69.57\t26.09\n+chr21.9809664\tchr21\t9809664\tF\t10\t80.00\t20.00\n+chr21.9817117\tchr21\t9817117\tF\t28\t17.86\t82.14\n+chr21.9817099\tchr21\t9817099\tF\t28\t89.29\t10.71\n+chr21.9826907\tchr21\t9826907\tF\t228\t4.39\t95.61\n+chr21.9833134\tchr21\t9833134\tF\t14\t28.57\t71.43\n+chr21.9834252\tchr21\t9834252\tF\t10\t100.00\t0.00\n+chr21.9833149\tchr21\t9833149\tF\t14\t50.00\t50.00\n+chr21.9820652\tchr21\t9820652\tF\t291\t43.30\t56.70\n+chr21.9820622\tchr21\t9820622\tF\t301\t1.00\t99.00\n+chr21.9831075\tchr21\t9831075\tF\t26\t38.46\t61.54\n+chr21.9822476\tchr21\t9822476\tF\t16\t68.75\t31.25\n+chr21.9827226\tchr21\t9827226\tF\t10\t30.00\t70.00\n+chr21.9822490\tchr21\t9822490\tF\t16\t6.25\t93.75\n+chr21.9822455\tchr21\t9822455\tF\t14\t92.86\t7.14\n+chr21.9827256\tchr21\t9827256\tF\t11\t18.18\t81.82\n+chr21.9825538\tchr21\t9825538\tF\t13\t53.85\t46.15\n+chr21.9829382\tchr21\t9829382\tF\t10\t100.00\t0.00\n+chr21.9840137\tchr21\t9840137\tF\t11\t45.45\t54.55\n+chr21.9835776\tchr21\t9835776\tF\t10\t100.00\t0.00\n+chr21.9835751\tchr21\t9835751\tF\t12\t91.67\t8.33\n+chr21.9844689\tchr21\t9844689\tF\t11\t18.18\t81.82\n+chr21.9842880\tchr21\t9842880\tF\t18\t44.44\t55.56\n+chr21.9849022\tchr21\t9849022\tF\t515\t82.91\t17.09\n+chr21.9848922\tchr21\t9848922\tF\t20\t70.00\t30.00\n+chr21.9841811\tchr21\t9841811\tF\t17\t52.94\t47.06\n+chr21.9843410\tchr21\t9843410\tF\t10\t80.00\t20.00\n+chr21.9844694\tchr21\t9844694\tF\t11\t9.09\t90.91\n+chr21.9842905\tchr21\t9842905\tF\t14\t71.43\t28.57\n+chr21.9847953\tchr21\t9847953\tF\t18\t88.89\t11.11\n+chr21.9844705\tchr21\t9844705\tF\t11\t63.64\t36.36\n+chr21.9853296\tchr21\t9853296\tF\t333\t80.48\t19.52\n+chr21.9853326\tchr21\t9853326\tF\t329\t75.68\t24.01\n+chr21.9863481\tchr21\t9863481\tF\t11\t90.91\t9.09\n+chr21.9862041\tchr21\t9862041\tF\t16\t25.00\t75.00\n+chr21.9852324\tchr21\t9852324\tF\t10\t100.00\t0.00\n+chr21.9860847\tchr21\t9860847\tF\t11\t90.91\t9.09\n+chr21.9859015\tchr21\t9859015\tF\t10\t90.00\t10.00\n+chr21.9860126\tchr21\t9860126\tF\t83\t93.98\t6.02\n+chr21.9857426\tchr21\t9857426\tF\t11\t54.55\t45.45\n+chr21.9860872\tchr21\t9860872\tF\t13\t92.31\t7.69\n+chr21.9852349\tchr21\t9852349\tF\t11\t63.64\t36.36\n+chr21.9874763\tchr21\t9874763\tF\t11\t36.36\t63.64\n+chr21.9874238\tchr21\t9874238\tR\t10\t100.00\t0.00\n+chr21.9866171\tchr21\t9866171\tF\t10\t90.00\t10.00\n+chr21.9874209\tchr21\t9874209\tR\t10\t100.00\t0.00\n+chr21.9874437\tchr21\t9874437\tF\t82\t95.12\t4.88\n+chr21.9875688\tchr21\t9875688\tF\t10\t40.00\t60.00\n+chr21.9874403\tchr21\t9874403\tF\t11\t72.73\t27.27\n+chr21.9876600\tchr21\t9876600\tF\t10\t100.00\t0.00\n+chr21.9878825\tchr21\t9878825\tF\t13\t84.62\t15.38\n+chr21.9881469\tchr21\t9881469\tF\t10\t30.00\t70.00\n+chr21.9882409\tchr21\t9882409\tF\t10\t70.00\t30.00\n+chr21.9880919\tchr21\t9880919\tF\t10\t70.00\t30.00\n+chr21.9880285\tchr21\t9880285\tF\t17\t47.06\t52.94\n+chr21.9881324\tchr21\t9881324\tF\t10\t60.00\t40.00\n+chr21.9906644\tchr21\t9906644\tF\t108\t85.19\t14.81\n+chr21.9906824\tchr21\t9906824\tR\t16\t93.75\t6.25\n+chr21.9906884\tchr21\t9906884\tF\t41\t41.46\t58.54\n+chr21.9906640\tchr21\t9906640\tF\t112\t12.50\t87.50\n+chr21.9906827\tchr21\t9906827\tR\t16\t100.00\t0.00\n+chr21.9906910\tchr21\t9906910\tR\t16\t93.75\t6.25\n+chr21.9906822\tchr21\t9906822\tR\t16\t100.00\t0.00\n+chr21.9906864\tchr21\t9906864\tF\t41\t82.93\t17.07\n+chr21.9906839\tchr21\t9906839\tR\t15\t93.33\t6.67\n+chr21.9906805\tchr21\t9906805\tR\t16\t81.25\t18.75\n+chr21.9906869\tchr21\t9906869\tF\t40\t15.00\t85.00\n+chr21.9906641\tchr21\t9906641\tR\t35\t8.57\t91.43\n+chr21.9906926\tchr21\t9906926\tR\t15\t86.67\t13.33\n+chr21.9906676\tchr21\t9906676\tF\t60\t96.67\t3.33\n+chr21.9906847\tchr21\t9906847\tR\t15'..b'8566739\tchr21\t18566739\tF\t12\t100.00\t0.00\n+chr21.18566677\tchr21\t18566677\tF\t15\t100.00\t0.00\n+chr21.18566634\tchr21\t18566634\tF\t19\t94.74\t5.26\n+chr21.18566639\tchr21\t18566639\tF\t19\t94.74\t5.26\n+chr21.18574487\tchr21\t18574487\tR\t19\t100.00\t0.00\n+chr21.18574453\tchr21\t18574453\tR\t22\t86.36\t13.64\n+chr21.18574312\tchr21\t18574312\tF\t15\t73.33\t26.67\n+chr21.18576203\tchr21\t18576203\tR\t22\t68.18\t31.82\n+chr21.18576145\tchr21\t18576145\tF\t70\t88.57\t11.43\n+chr21.18576211\tchr21\t18576211\tR\t22\t90.91\t9.09\n+chr21.18576179\tchr21\t18576179\tR\t22\t90.91\t9.09\n+chr21.18576178\tchr21\t18576178\tF\t62\t79.03\t20.97\n+chr21.18576141\tchr21\t18576141\tF\t70\t74.29\t25.71\n+chr21.18576157\tchr21\t18576157\tF\t64\t92.19\t7.81\n+chr21.18578901\tchr21\t18578901\tF\t12\t83.33\t16.67\n+chr21.18578884\tchr21\t18578884\tF\t12\t100.00\t0.00\n+chr21.18582975\tchr21\t18582975\tF\t13\t30.77\t69.23\n+chr21.18582970\tchr21\t18582970\tF\t13\t15.38\t84.62\n+chr21.18615698\tchr21\t18615698\tR\t37\t64.86\t35.14\n+chr21.18641515\tchr21\t18641515\tF\t14\t35.71\t64.29\n+chr21.18713624\tchr21\t18713624\tF\t25\t100.00\t0.00\n+chr21.18713634\tchr21\t18713634\tF\t25\t92.00\t8.00\n+chr21.18713648\tchr21\t18713648\tF\t25\t88.00\t12.00\n+chr21.18737989\tchr21\t18737989\tR\t17\t0.00\t100.00\n+chr21.18738234\tchr21\t18738234\tR\t18\t33.33\t66.67\n+chr21.18957876\tchr21\t18957876\tF\t30\t93.33\t6.67\n+chr21.18958033\tchr21\t18958033\tR\t35\t91.43\t8.57\n+chr21.19047280\tchr21\t19047280\tF\t14\t85.71\t14.29\n+chr21.19053688\tchr21\t19053688\tF\t10\t100.00\t0.00\n+chr21.19053696\tchr21\t19053696\tF\t10\t100.00\t0.00\n+chr21.19053729\tchr21\t19053729\tF\t11\t27.27\t72.73\n+chr21.19059419\tchr21\t19059419\tR\t18\t5.56\t94.44\n+chr21.19086113\tchr21\t19086113\tF\t13\t76.92\t23.08\n+chr21.19086074\tchr21\t19086074\tF\t16\t100.00\t0.00\n+chr21.19086082\tchr21\t19086082\tF\t16\t100.00\t0.00\n+chr21.19095152\tchr21\t19095152\tF\t23\t47.83\t52.17\n+chr21.19095182\tchr21\t19095182\tF\t23\t78.26\t21.74\n+chr21.19095158\tchr21\t19095158\tF\t23\t60.87\t39.13\n+chr21.19141969\tchr21\t19141969\tF\t16\t100.00\t0.00\n+chr21.19142010\tchr21\t19142010\tF\t16\t50.00\t50.00\n+chr21.19178253\tchr21\t19178253\tR\t13\t92.31\t7.69\n+chr21.19235222\tchr21\t19235222\tF\t11\t81.82\t18.18\n+chr21.19235258\tchr21\t19235258\tF\t11\t45.45\t54.55\n+chr21.19282009\tchr21\t19282009\tF\t19\t26.32\t73.68\n+chr21.19329763\tchr21\t19329763\tR\t16\t100.00\t0.00\n+chr21.19390691\tchr21\t19390691\tR\t59\t88.14\t11.86\n+chr21.19390694\tchr21\t19390694\tR\t59\t81.36\t18.64\n+chr21.19421519\tchr21\t19421519\tF\t44\t84.09\t15.91\n+chr21.19421563\tchr21\t19421563\tF\t36\t100.00\t0.00\n+chr21.19528262\tchr21\t19528262\tR\t11\t90.91\t9.09\n+chr21.19528268\tchr21\t19528268\tR\t11\t100.00\t0.00\n+chr21.19528225\tchr21\t19528225\tR\t11\t90.91\t9.09\n+chr21.19539511\tchr21\t19539511\tR\t40\t82.50\t17.50\n+chr21.19539528\tchr21\t19539528\tR\t39\t94.87\t5.13\n+chr21.19539486\tchr21\t19539486\tR\t38\t94.74\t5.26\n+chr21.19539361\tchr21\t19539361\tF\t14\t85.71\t14.29\n+chr21.19579357\tchr21\t19579357\tR\t19\t100.00\t0.00\n+chr21.19579345\tchr21\t19579345\tR\t14\t100.00\t0.00\n+chr21.19579352\tchr21\t19579352\tR\t19\t100.00\t0.00\n+chr21.19579289\tchr21\t19579289\tF\t35\t91.43\t8.57\n+chr21.19579361\tchr21\t19579361\tR\t19\t100.00\t0.00\n+chr21.19599501\tchr21\t19599501\tF\t12\t100.00\t0.00\n+chr21.19626384\tchr21\t19626384\tR\t11\t90.91\t9.09\n+chr21.19626227\tchr21\t19626227\tR\t42\t97.62\t2.38\n+chr21.19711774\tchr21\t19711774\tF\t29\t79.31\t20.69\n+chr21.19711822\tchr21\t19711822\tF\t28\t89.29\t10.71\n+chr21.19739452\tchr21\t19739452\tF\t13\t100.00\t0.00\n+chr21.19739521\tchr21\t19739521\tR\t41\t95.12\t4.88\n+chr21.19788093\tchr21\t19788093\tR\t29\t100.00\t0.00\n+chr21.19788117\tchr21\t19788117\tR\t29\t96.55\t3.45\n+chr21.19788113\tchr21\t19788113\tR\t29\t100.00\t0.00\n+chr21.19788122\tchr21\t19788122\tR\t29\t96.55\t3.45\n+chr21.19788076\tchr21\t19788076\tR\t29\t96.55\t3.45\n+chr21.19788089\tchr21\t19788089\tR\t28\t96.43\t3.57\n+chr21.19788073\tchr21\t19788073\tR\t29\t100.00\t0.00\n+chr21.19829742\tchr21\t19829742\tF\t25\t92.00\t8.00\n+chr21.19855690\tchr21\t19855690\tF\t19\t89.47\t10.53\n+chr21.19855711\tchr21\t19855711\tF\t18\t83.33\t16.67\n+chr21.19855706\tchr21\t19855706\tF\t19\t100.00\t0.00\n+chr21.19886045\tchr21\t19886045\tR\t30\t93.33\t6.67\n+chr21.19886061\tchr21\t19886061\tR\t31\t87.10\t12.90\n+chr21.19885992\tchr21\t19885992\tF\t20\t100.00\t0.00\n+chr21.19943653\tchr21\t19943653\tF\t32\t93.75\t6.25\n+chr21.19943695\tchr21\t19943695\tF\t32\t100.00\t0.00\n' |
| b |
| diff -r 000000000000 -r a8705df7c57f test-data/output_MethPerChr.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_MethPerChr.tsv Wed Dec 21 17:30:57 2016 -0500 |
| b |
| @@ -0,0 +1,2 @@ +diffMeth.per.chr.chr diffMeth.per.chr.number.of.hypermethylated diffMeth.per.chr.percentage.of.hypermethylated diffMeth.per.chr.number.of.hypomethylated diffMeth.per.chr.percentage.of.hypomethylated diffMeth.all.number.of.hypermethylated diffMeth.all.percentage.of.hypermethylated diffMeth.all.number.of.hypomethylated diffMeth.all.percentage.of.hypomethylated +chr21 72 7.47663551401869 54 5.60747663551402 72 7.47663551401869 54 5.60747663551402 |
| b |
| diff -r 000000000000 -r a8705df7c57f test-data/output_MethylDiff.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_MethylDiff.bedgraph Wed Dec 21 17:30:57 2016 -0500 |
| b |
| @@ -0,0 +1,127 @@ +track type=bedGraph name='output_MethylDiff.bedgraph' description='meth.diff' visibility=full color=255,0,255 altColor=102,205,170 maxHeightPixels=80:80:11 +chr21 9906680 9906681 35.1653301653302 +chr21 9906699 9906700 28.5704970446562 +chr21 9906872 9906873 44.3348115299335 +chr21 9927526 9927527 -47.0798319327731 +chr21 9944504 9944505 -55.4299108078178 +chr21 9944662 9944663 -33.0342507663848 +chr21 9959406 9959407 -36.9709316107621 +chr21 9959540 9959541 -36.4372469635627 +chr21 9959643 9959644 -40.8752458951712 +chr21 9959649 9959650 -34.0772217847152 +chr21 9967633 9967634 -38.734387197502 +chr21 10011840 10011841 43.8274153592073 +chr21 10011860 10011861 28.4593280282936 +chr21 10011924 10011925 25.0205352411235 +chr21 10011953 10011954 26.2227990611449 +chr21 10011963 10011964 37.7428356034944 +chr21 10011989 10011990 28.2085593731163 +chr21 10012068 10012069 44.7731476273251 +chr21 10012100 10012101 39.049677851389 +chr21 10012698 10012699 41.6204135169653 +chr21 10012933 10012934 37.5595238095238 +chr21 10012939 10012940 25.0292397660819 +chr21 10012941 10012942 52.0168422098569 +chr21 10012943 10012944 33.2451923076923 +chr21 10077698 10077699 -41.2090650514589 +chr21 10077704 10077705 -30.0312453503943 +chr21 10114304 10114305 -34.1442892946652 +chr21 10114350 10114351 -36.7417026642698 +chr21 10133110 10133111 -29.0386977886978 +chr21 10133158 10133159 -26.6887755102041 +chr21 10133159 10133160 -33.9783281733746 +chr21 10145438 10145439 -34.1156462585034 +chr21 10145470 10145471 -28.9036481001957 +chr21 10156519 10156520 -35.3716690707561 +chr21 10156520 10156521 -40 +chr21 10186518 10186519 -36.188545551837 +chr21 10186540 10186541 -52.1118147389334 +chr21 10190549 10190550 44.8701298701299 +chr21 10190880 10190881 -29.8343666076224 +chr21 10191429 10191430 -38.8120416527835 +chr21 10191768 10191769 -28.6890645586298 +chr21 10191818 10191819 -25.6350553803864 +chr21 10191922 10191923 33.099059966141 +chr21 13282439 13282440 -26.3767547789725 +chr21 13664887 13664888 -38.6112765535041 +chr21 13664888 13664889 -38.5541849216532 +chr21 13666552 13666553 -28.212481962482 +chr21 13673753 13673754 33.1681681681682 +chr21 13958265 13958266 -43.2909604519774 +chr21 13991067 13991068 37.9166666666667 +chr21 13991084 13991085 49.5253623188406 +chr21 13991219 13991220 36.6655115669298 +chr21 13998986 13998987 56.729658253524 +chr21 13999004 13999005 40.3943216730128 +chr21 13999010 13999011 35.0576176133985 +chr21 13999011 13999012 52.5019425019425 +chr21 13999022 13999023 55.8704301695306 +chr21 13999058 13999059 26.4973704185643 +chr21 13999081 13999082 55.1275510204082 +chr21 13999088 13999089 54.4328429046037 +chr21 13999094 13999095 34.5535714285714 +chr21 13999106 13999107 51.8542358803987 +chr21 13999113 13999114 46.1999423797177 +chr21 13999141 13999142 45.1480836236934 +chr21 13999209 13999210 52.0545532814151 +chr21 13999238 13999239 58.2001332001332 +chr21 13999246 13999247 53.5700651532119 +chr21 13999248 13999249 55.6165377176016 +chr21 13999255 13999256 40.4911754911755 +chr21 13999262 13999263 39.4345238095238 +chr21 13999565 13999566 32.2612270714737 +chr21 13999566 13999567 35.8899320743981 +chr21 13999567 13999568 47.3152173913043 +chr21 13999573 13999574 43.7272727272727 +chr21 13999574 13999575 45.6695156695157 +chr21 14000091 14000092 -27.547619047619 +chr21 14018049 14018050 66.6543209876543 +chr21 14018260 14018261 35.7126026147765 +chr21 14057233 14057234 -43.533724340176 +chr21 14230283 14230284 -55.3493107769424 +chr21 14230705 14230706 -32.1428571428571 +chr21 14305243 14305244 -28.8461538461539 +chr21 14367278 14367279 42.5185185185185 +chr21 14568170 14568171 28.1229156002296 +chr21 14568175 14568176 28.2671957671958 +chr21 14568182 14568183 28.4867728737257 +chr21 14568203 14568204 25.5965317197929 +chr21 15447184 15447185 -62.524975024975 +chr21 15583672 15583673 -36.7424242424242 +chr21 15583715 15583716 -33.1168831168831 +chr21 16454614 16454615 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18539240 43.0909090909091 +chr21 18539248 18539249 54.389880952381 +chr21 18539249 18539250 47.3246753246753 +chr21 18539252 18539253 69.9848024316109 +chr21 18539258 18539259 47.3412698412698 +chr21 18539265 18539266 66.1674347158218 +chr21 18539932 18539933 54.4904279279279 +chr21 18539959 18539960 44.758064516129 +chr21 18582969 18582970 -58.974358974359 +chr21 18582974 18582975 -47.5380899293943 +chr21 18615697 18615698 -31.4564564564565 |
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| diff -r 000000000000 -r a8705df7c57f test-data/output_myDiff.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_myDiff.bedgraph Wed Dec 21 17:30:57 2016 -0500 |
| b |
| b"@@ -0,0 +1,964 @@\n+track type=bedGraph name='output_myDiff.bedgraph' description='meth.diff' visibility=full color=255,0,255 altColor=102,205,170 maxHeightPixels=80:80:11 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|
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| diff -r 000000000000 -r a8705df7c57f test-data/output_seg_diff.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_seg_diff.bed Wed Dec 21 17:30:57 2016 -0500 |
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| @@ -0,0 +1,4 @@ +track name="meth segments" description="meth segments" itemRgb=on +chr21 9853000 13991000 1 -10.9674674784423 . 9853000 13991000 190,190,190 +chr21 13991000 14019000 2 17.5358121475575 . 13991000 14019000 0,100,0 +chr21 14057000 19944000 1 -7.21990925670131 . 14057000 19944000 140,207,140 |
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| diff -r 000000000000 -r a8705df7c57f test-data/output_seg_raw.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_seg_raw.bed Wed Dec 21 17:30:57 2016 -0500 |
| b |
| @@ -0,0 +1,6 @@ +track name="meth segments" description="meth segments" itemRgb=on +chr21 9764000 14382000 2 68.3360848593166 . 9764000 14382000 0,227,0 +chr21 14510000 14774000 1 37.2301737330093 . 14510000 14774000 162,199,162 +chr21 14791000 15242000 3 93.231961836613 . 14791000 15242000 0,100,0 +chr21 15286000 15583000 1 32.8700430825969 . 15286000 15583000 190,190,190 +chr21 15583000 19944000 2 67.8414022933781 . 15583000 19944000 0,230,0 |
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| diff -r 000000000000 -r a8705df7c57f test-data/output_statistics.pdf |
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| Binary file test-data/output_statistics.pdf has changed |
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| diff -r 000000000000 -r a8705df7c57f test-data/test.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.r Wed Dec 21 17:30:57 2016 -0500 |
| [ |
| @@ -0,0 +1,60 @@ +library("methylKit") + +file.list = list("input_test1.myCpG.txt", "input_test2.myCpG.txt", "input_control1.myCpG.txt", "input_control2.myCpG.txt") + +myobj=methRead( file.list, + sample.id=list("test 1","test 2","control 1","control 2"),assembly="hg18",pipeline="amp",treatment=c(1,1,0,0)) + +pdf('output_statistics.pdf') +for (obj in myobj){ + getMethylationStats(obj,plot=TRUE,both.strands=FALSE) + getCoverageStats(obj,plot=TRUE,both.strands=FALSE) +} +devname = dev.off() + +# unite function +methidh = unite(myobj) + +pdf("output_correlation.pdf") +getCorrelation(object = methidh, plot=TRUE, method = "pearson") +devname = dev.off() + +# differential methylation +myDiff = calculateDiffMeth(methidh, overdispersion="none", + adjust="SLIM", effect="wmean", test="Chisq", + slim=FALSE, weighted.mean=FALSE) + +bedgraph(myDiff, file.name="output_myDiff.bedgraph", col.name="meth.diff", + unmeth=FALSE, log.transform=FALSE, negative=FALSE, add.on="") + +MethPerChr = diffMethPerChr(myDiff, plot=FALSE, + qvalue.cutoff=0.01, + meth.cutoff=25) +write.table(MethPerChr, sep="\t", row.names=FALSE, quote=FALSE, file="output_MethPerChr.tsv") + +MethylDiff = getMethylDiff(myDiff, difference=25, + qvalue=0.01, type="all") +bedgraph(MethylDiff, file.name="output_MethylDiff.bedgraph", col.name="meth.diff", + unmeth=FALSE,log.transform=FALSE,negative=FALSE,add.on="") + +pdf( "output_clustering.pdf" ) +methClust = clusterSamples(methidh, dist="correlation", method="ward") +devname = dev.off() + +pdf( "output_PCA.pdf" ) +PCASamples(methidh) +devname = dev.off() + +## methSeg works for methylRaw or methylDiff with resolution region, +## so methylBase has to be tiled before +tileRaw = tileMethylCounts(myobj[[1]]) +tileBase = tileMethylCounts(methidh) +tileDiff = calculateDiffMeth(tileBase) + +## methseg generates Granges +segRaw = methSeg(tileRaw, diagnostic.plot = FALSE) +segDiff = methSeg(tileDiff, diagnostic.plot = FALSE) + +## and can be exported as BED +methSeg2bed(segments = segRaw, filename = "output_seg_raw.bed") +methSeg2bed(segments = segDiff, filename = "output_seg_diff.bed") |