# HG changeset patch
# User fabio
# Date 1496243242 14400
# Node ID 565118df598a1cbcde57b76702e66727aaa18d1b
# Parent 81faa1567178a2f4e13c3831392ab6c499385338
Uploaded 20170531
diff -r 81faa1567178 -r 565118df598a ._ETn_example
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diff -r 81faa1567178 -r 565118df598a ._example
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diff -r 81faa1567178 -r 565118df598a ._loadandplot.R
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diff -r 81faa1567178 -r 565118df598a ._plotwithscale.R
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diff -r 81faa1567178 -r 565118df598a ._testandplot.R
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diff -r 81faa1567178 -r 565118df598a ETn_example/._.DS_Store
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diff -r 81faa1567178 -r 565118df598a ETn_example/._Control.bed
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diff -r 81faa1567178 -r 565118df598a ETn_example/._DESCRIPTION.txt
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diff -r 81faa1567178 -r 565118df598a ETn_example/._ETn_fixed.bed
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diff -r 81faa1567178 -r 565118df598a ETn_example/._Recombination_hotspots.txt
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diff -r 81faa1567178 -r 565118df598a ETn_example/._features.header
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diff -r 81faa1567178 -r 565118df598a ETn_example/._regions.header
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diff -r 81faa1567178 -r 565118df598a ETn_example/Control.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ETn_example/Control.bed Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,1142 @@
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diff -r 81faa1567178 -r 565118df598a ETn_example/DESCRIPTION.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ETn_example/DESCRIPTION.txt Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,21 @@
+This example contains two region datasets "ETn fixed", "Control" and one feature "Recombination hotspots content".
+In particular, the region dataset "ETn fixed" contains 1296 genomic regions of 64 kb surrounding
+fixed ETns elements (32-kb flanking sequences upstream and 32-kb flanking sequences downstream
+of each element). The region dataset "Control" contains 1142 regions of 64 kb without elements,
+used as control in the test. The regions are aligned around their center (i.e. around the ETn integration
+sites).
+Recombination hotspots measurements are associated to each "ETn fixed" and "Control" region. In
+particular, this feature is measured in 1-kb windows, so that each region is associated to a recombination
+hotspots curve made of 64 values. The measurement used is the feature content, i.e. the
+fraction of the 1-kb window that is covered by recombination hotspots
+
+Data have been collected and pre-processed by: R Campos-Sanchez, MA Cremona, A Pini, F
+Chiaromonte and KD Makova (2016). Integration and fixation preferences of human and mouse
+endogenous retroviruses uncovered with Functional Data Analysis. PLoS Computational Biology.
+12(6): 1-41.
+Fixed ETn positions come from: Y Zhang, IA Maksakova, L Gagnier, LN van de Lagemaat, DL
+Mager (2008). Genome-wide assessments reveal extremely high levels of polymorphism of two
+active families of mouse endogenous retroviral elements. PLoS Genetics. 4: e1000007.
+Recombination hotspots data come from: H Brunschwig, L Levi, E Ben-David, RW Williams,
+B Yakir, S Shifman (2012). Fine-scale maps of recombination rates and hotspots in the mouse
+genome. Genetics. 191: 757-764.
\ No newline at end of file
diff -r 81faa1567178 -r 565118df598a ETn_example/ETn_fixed.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ETn_example/ETn_fixed.bed Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,1296 @@
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diff -r 81faa1567178 -r 565118df598a ETn_example/Recombination_hotspots.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ETn_example/Recombination_hotspots.txt Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,2438 @@
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diff -r 81faa1567178 -r 565118df598a ETn_example/features.header
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ETn_example/features.header Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,1 @@
+Recombination_hotspots.txt Recomb_hot Recombination hotspots
\ No newline at end of file
diff -r 81faa1567178 -r 565118df598a ETn_example/regions.header
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ETn_example/regions.header Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,2 @@
+Control.bed Control Control
+ETn_fixed.bed ETn_fixed ETn fixed
\ No newline at end of file
diff -r 81faa1567178 -r 565118df598a example/._.DS_Store
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diff -r 81faa1567178 -r 565118df598a example/._Controls_regions.bed
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diff -r 81faa1567178 -r 565118df598a example/._DESCRIPTION.txt
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diff -r 81faa1567178 -r 565118df598a example/._Elements1_regions.bed
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diff -r 81faa1567178 -r 565118df598a example/._Elements2_regions.bed
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diff -r 81faa1567178 -r 565118df598a example/._Elements3_regions.bed
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diff -r 81faa1567178 -r 565118df598a example/._Feature1.bed
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diff -r 81faa1567178 -r 565118df598a example/._Feature2.bed
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diff -r 81faa1567178 -r 565118df598a example/._features.header.bed.txt
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diff -r 81faa1567178 -r 565118df598a example/._regions.header.txt
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diff -r 81faa1567178 -r 565118df598a example/Controls_regions.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/example/Controls_regions.bed Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,35 @@
+chr1 91399892 91499892
+chr1 116447079 116547079
+chr2 231381109 231481109
+chr3 47386633 47486633
+chr3 99195712 99295712
+chr3 116765114 116865114
+chr3 134345017 134445017
+chr4 68064019 68164019
+chr4 137465811 137565811
+chr4 173293016 173393016
+chr5 59044110 59144110
+chr5 94592763 94692763
+chr5 108436006 108536006
+chr5 110836898 110936898
+chr5 146661073 146761073
+chr6 99727306 99827306
+chr7 88291325 88391325
+chr7 120999784 121099784
+chr8 126860366 126960366
+chr8 127636547 127736547
+chr11 41362564 41462564
+chr11 101741527 101841527
+chr12 15210277 15310277
+chr13 91106037 91206037
+chr13 91518822 91618822
+chr13 98959030 99059030
+chr15 39087176 39187176
+chr17 58542142 58642142
+chr18 12199823 12299823
+chr20 8173704 8273704
+chr21 16255112 16355112
+chr21 45089115 45189115
+chrX 23898983 23998983
+chrX 37029585 37129585
+chrX 103593349 103693349
diff -r 81faa1567178 -r 565118df598a example/DESCRIPTION.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/example/DESCRIPTION.txt Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,2 @@
+This example contains simulated measurements of two different genomic features, "ftr1" and "ftr2",
+corresponding to four different region datasets: "elem1", "elem2", "elem3" and "control".
diff -r 81faa1567178 -r 565118df598a example/Elements1_regions.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/example/Elements1_regions.bed Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,25 @@
+chr2 49960150 50060150
+chr2 55912445 56012445
+chr3 140326750 140426750
+chr4 41772201 41872201
+chr4 70629719 70729719
+chr4 109340735 109440735
+chr5 15025389 15125389
+chr5 43028888 43128888
+chr5 58231354 58331354
+chr5 91277761 91377761
+chr5 119464508 119564508
+chr6 85309170 85409170
+chr6 85762072 85862072
+chr6 134621363 134721363
+chr6 147470164 147570164
+chr7 77195798 77295798
+chr7 77880914 77980914
+chr7 114805399 114905399
+chr10 46350885 46450885
+chr10 67833078 67933078
+chr12 27722692 27822692
+chr12 95518506 95618506
+chr12 117863466 117963466
+chr14 100464166 100564166
+chrX 29266748 29366748
diff -r 81faa1567178 -r 565118df598a example/Elements2_regions.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/example/Elements2_regions.bed Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,20 @@
+chr1 65942901 66042901
+chr1 117128102 117228102
+chr1 190338169 190438169
+chr2 227365478 227465478
+chr6 50856764 50956764
+chr6 135703067 135803067
+chr7 38228726 38328726
+chr7 51115898 51215898
+chr7 150325760 150425760
+chr8 25475691 25575691
+chr9 73374609 73474609
+chr11 55092625 55192625
+chr11 86581661 86681661
+chr12 12795284 12895284
+chr12 48151882 48251882
+chr12 83109951 83209951
+chr15 31430278 31530278
+chr15 65610815 65710815
+chr17 40766223 40866223
+chr20 17245048 17345048
diff -r 81faa1567178 -r 565118df598a example/Elements3_regions.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/example/Elements3_regions.bed Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,28 @@
+chr1 49721616 49821616
+chr1 95059425 95159425
+chr1 207236313 207336313
+chr2 73790843 73890843
+chr3 134465321 134565321
+chr4 43433669 43533669
+chr4 122032777 122132777
+chr5 12701747 12801747
+chr5 58501529 58601529
+chr5 152853250 152953250
+chr6 136085023 136185023
+chr6 147019529 147119529
+chr7 14192964 14292964
+chr7 125519883 125619883
+chr8 77652872 77752872
+chr8 108375665 108475665
+chr9 2984971 3084971
+chr10 978822 1078822
+chr11 18395046 18495046
+chr12 47273592 47373592
+chr12 60095778 60195778
+chr12 84854096 84954096
+chr12 95157539 95257539
+chr14 23982000 24082000
+chr16 1875335 1975335
+chr16 66789863 66889863
+chr18 64644131 64744131
+chr21 15966609 16066609
diff -r 81faa1567178 -r 565118df598a example/Feature1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/example/Feature1.bed Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,5400 @@
+chr1 91399892 91401892 0.914729028492568
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diff -r 81faa1567178 -r 565118df598a example/Feature2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/example/Feature2.bed Wed May 31 11:07:22 2017 -0400
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diff -r 81faa1567178 -r 565118df598a example/features.header.bed.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/example/features.header.bed.txt Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,2 @@
+Feature1.bed ftr1 Feature 1
+Feature2.bed ftr2 Feature 2
\ No newline at end of file
diff -r 81faa1567178 -r 565118df598a example/regions.header.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/example/regions.header.txt Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,4 @@
+Elements1_regions.bed elem1 Elements 1
+Elements2_regions.bed elem2 Elements 2
+Elements3_regions.bed elem3 Elements 3
+Controls_regions.bed control Controls
\ No newline at end of file
diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/._.DS_Store
Binary file iwtomics/ETn_example/._.DS_Store has changed
diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/._Control.bed
Binary file iwtomics/ETn_example/._Control.bed has changed
diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/._DESCRIPTION.txt
Binary file iwtomics/ETn_example/._DESCRIPTION.txt has changed
diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/._ETn_fixed.bed
Binary file iwtomics/ETn_example/._ETn_fixed.bed has changed
diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/._Recombination_hotspots.txt
Binary file iwtomics/ETn_example/._Recombination_hotspots.txt has changed
diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/._features.header
Binary file iwtomics/ETn_example/._features.header has changed
diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/._regions.header
Binary file iwtomics/ETn_example/._regions.header has changed
diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/Control.bed
--- a/iwtomics/ETn_example/Control.bed Wed May 31 11:06:30 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1142 +0,0 @@
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diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/DESCRIPTION.txt
--- a/iwtomics/ETn_example/DESCRIPTION.txt Wed May 31 11:06:30 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-This example contains two region datasets "ETn fixed", "Control" and one feature "Recombination hotspots content".
-In particular, the region dataset "ETn fixed" contains 1296 genomic regions of 64 kb surrounding
-fixed ETns elements (32-kb flanking sequences upstream and 32-kb flanking sequences downstream
-of each element). The region dataset "Control" contains 1142 regions of 64 kb without elements,
-used as control in the test. The regions are aligned around their center (i.e. around the ETn integration
-sites).
-Recombination hotspots measurements are associated to each "ETn fixed" and "Control" region. In
-particular, this feature is measured in 1-kb windows, so that each region is associated to a recombination
-hotspots curve made of 64 values. The measurement used is the feature content, i.e. the
-fraction of the 1-kb window that is covered by recombination hotspots
-
-Data have been collected and pre-processed by: R Campos-Sanchez, MA Cremona, A Pini, F
-Chiaromonte and KD Makova (2016). Integration and fixation preferences of human and mouse
-endogenous retroviruses uncovered with Functional Data Analysis. PLoS Computational Biology.
-12(6): 1-41.
-Fixed ETn positions come from: Y Zhang, IA Maksakova, L Gagnier, LN van de Lagemaat, DL
-Mager (2008). Genome-wide assessments reveal extremely high levels of polymorphism of two
-active families of mouse endogenous retroviral elements. PLoS Genetics. 4: e1000007.
-Recombination hotspots data come from: H Brunschwig, L Levi, E Ben-David, RW Williams,
-B Yakir, S Shifman (2012). Fine-scale maps of recombination rates and hotspots in the mouse
-genome. Genetics. 191: 757-764.
\ No newline at end of file
diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/ETn_fixed.bed
--- a/iwtomics/ETn_example/ETn_fixed.bed Wed May 31 11:06:30 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1296 +0,0 @@
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diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/Recombination_hotspots.txt
--- a/iwtomics/ETn_example/Recombination_hotspots.txt Wed May 31 11:06:30 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,2438 +0,0 @@
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-chr9 47502414 47566414 1 1 1 1 1 1 1 1 1 1 1 0.774 0.226 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0.774 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.226 1 1 1 0.774 0 0 0 0 0 0 0 0.226 1 1 1
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-chr9 47630414 47694414 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0.774 0 0 0 0 0 0.226 1 1 1 1 1 1 0.774 0 0 0 0 0.226 1 1 1 1 1 1 1 1 0.774 0 0.226 1 1 1 1 1 1 1 0.774 0.226 1 1 1 1
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-chr9 69176049 69240049 1 1 1 1 0.233 0 0 0 0 0 0 0.767 1 1 0.233 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.767 1 1 0.233 0 0 0 0 0.767 1 1 1 1 0.233 0 0 0 0
-chr9 69240049 69304049 0 0 0 0 0 0.767 1 1 1 1 0.233 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.767 1 0.233 0 0 0 0 0 0 0 0 0 0 0
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-chr9 74791622 74855622 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.34 1 1 0.66 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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-chr9 79932960 79996960 0.322 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.678 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0.322 0 0 0 0 0 0 0.678 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
-chr9 84626957 84690957 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.675 1 1 0.325 0 0 0 0
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-chr9 107376141 107440141 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0.689 0 0 0 0 0 0 0 0 0.311 1 1 0.689 0 0 0 0 0 0 0 0 0 0 0.311 1 1 1 1 1 1 1 1
-chr9 107462650 107526650 0 0 0 0 0 0 0 0 0 0 0.82 1 1 1 1 0.18 0 0 0 0 0 0 0 0.82 1 1 1 1 1 0.18 0.82 1 0.18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.82 1 1 0.18 0 0.82 1 1 0.18
-chr9 107526650 107590650 0 0 0.82 1 1 1 1 1 1 0.18 0 0.82 1 1 1 1 1 1 0.18 0 0.82 1 1 1 1 0.18 0 0 0 0.82 1 1 0.18 0 0.82 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0.18 0 0.82 1 0.18 0 0 0 0 0 0.82 1 1
-chr9 107590650 107654650 0.18 0.82 1 1 1 1 1 1 1 1 1 1 0.18 0 0 0 0 0 0 0 0 0 0 0 0 0.82 1 1 1 1 1 1 1 1 1 1 0.18 0 0 0 0 0 0.82 1 1 1 0.18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.82
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-chr9 110485254 110549254 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-chr9 110616374 110680374 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.544 1 1 1 1 1 1 1 1 1 0.456 0.544 1 1 1 1 1 1 0.456 0.544 1 1 0.456 0.544 1 1 1
-chr9 111968818 112032818 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-chr9 113836504 113900504 0 0 0.457 1 1 1 1 0.543 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.457 1 1 1 1 1 1 1 1 0.543 0 0 0 0 0.457 1 1 1 1
-chr9 118910538 118974538 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.491 1 1 1 1 1 1 1 1 0.509 0 0 0 0 0 0 0 0 0 0
-chr9 121627136 121691136 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/features.header
--- a/iwtomics/ETn_example/features.header Wed May 31 11:06:30 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-Recombination_hotspots.txt Recomb_hot Recombination hotspots
\ No newline at end of file
diff -r 81faa1567178 -r 565118df598a iwtomics/ETn_example/regions.header
--- a/iwtomics/ETn_example/regions.header Wed May 31 11:06:30 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-Control.bed Control Control
-ETn_fixed.bed ETn_fixed ETn fixed
\ No newline at end of file
diff -r 81faa1567178 -r 565118df598a iwtomics/example/._.DS_Store
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diff -r 81faa1567178 -r 565118df598a iwtomics/example/._Controls_regions.bed
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diff -r 81faa1567178 -r 565118df598a iwtomics/example/._DESCRIPTION.txt
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diff -r 81faa1567178 -r 565118df598a iwtomics/example/._Elements1_regions.bed
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diff -r 81faa1567178 -r 565118df598a iwtomics/example/._Elements2_regions.bed
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diff -r 81faa1567178 -r 565118df598a iwtomics/example/._Elements3_regions.bed
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diff -r 81faa1567178 -r 565118df598a iwtomics/example/._Feature1.bed
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diff -r 81faa1567178 -r 565118df598a iwtomics/example/._Feature2.bed
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diff -r 81faa1567178 -r 565118df598a iwtomics/example/._features.header.bed.txt
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diff -r 81faa1567178 -r 565118df598a iwtomics/example/._regions.header.txt
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diff -r 81faa1567178 -r 565118df598a iwtomics/example/Controls_regions.bed
--- a/iwtomics/example/Controls_regions.bed Wed May 31 11:06:30 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-chr1 91399892 91499892
-chr1 116447079 116547079
-chr2 231381109 231481109
-chr3 47386633 47486633
-chr3 99195712 99295712
-chr3 116765114 116865114
-chr3 134345017 134445017
-chr4 68064019 68164019
-chr4 137465811 137565811
-chr4 173293016 173393016
-chr5 59044110 59144110
-chr5 94592763 94692763
-chr5 108436006 108536006
-chr5 110836898 110936898
-chr5 146661073 146761073
-chr6 99727306 99827306
-chr7 88291325 88391325
-chr7 120999784 121099784
-chr8 126860366 126960366
-chr8 127636547 127736547
-chr11 41362564 41462564
-chr11 101741527 101841527
-chr12 15210277 15310277
-chr13 91106037 91206037
-chr13 91518822 91618822
-chr13 98959030 99059030
-chr15 39087176 39187176
-chr17 58542142 58642142
-chr18 12199823 12299823
-chr20 8173704 8273704
-chr21 16255112 16355112
-chr21 45089115 45189115
-chrX 23898983 23998983
-chrX 37029585 37129585
-chrX 103593349 103693349
diff -r 81faa1567178 -r 565118df598a iwtomics/example/DESCRIPTION.txt
--- a/iwtomics/example/DESCRIPTION.txt Wed May 31 11:06:30 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-This example contains simulated measurements of two different genomic features, "ftr1" and "ftr2",
-corresponding to four different region datasets: "elem1", "elem2", "elem3" and "control".
diff -r 81faa1567178 -r 565118df598a iwtomics/example/Elements1_regions.bed
--- a/iwtomics/example/Elements1_regions.bed Wed May 31 11:06:30 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-chr2 49960150 50060150
-chr2 55912445 56012445
-chr3 140326750 140426750
-chr4 41772201 41872201
-chr4 70629719 70729719
-chr4 109340735 109440735
-chr5 15025389 15125389
-chr5 43028888 43128888
-chr5 58231354 58331354
-chr5 91277761 91377761
-chr5 119464508 119564508
-chr6 85309170 85409170
-chr6 85762072 85862072
-chr6 134621363 134721363
-chr6 147470164 147570164
-chr7 77195798 77295798
-chr7 77880914 77980914
-chr7 114805399 114905399
-chr10 46350885 46450885
-chr10 67833078 67933078
-chr12 27722692 27822692
-chr12 95518506 95618506
-chr12 117863466 117963466
-chr14 100464166 100564166
-chrX 29266748 29366748
diff -r 81faa1567178 -r 565118df598a iwtomics/example/Elements2_regions.bed
--- a/iwtomics/example/Elements2_regions.bed Wed May 31 11:06:30 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-chr1 65942901 66042901
-chr1 117128102 117228102
-chr1 190338169 190438169
-chr2 227365478 227465478
-chr6 50856764 50956764
-chr6 135703067 135803067
-chr7 38228726 38328726
-chr7 51115898 51215898
-chr7 150325760 150425760
-chr8 25475691 25575691
-chr9 73374609 73474609
-chr11 55092625 55192625
-chr11 86581661 86681661
-chr12 12795284 12895284
-chr12 48151882 48251882
-chr12 83109951 83209951
-chr15 31430278 31530278
-chr15 65610815 65710815
-chr17 40766223 40866223
-chr20 17245048 17345048
diff -r 81faa1567178 -r 565118df598a iwtomics/example/Elements3_regions.bed
--- a/iwtomics/example/Elements3_regions.bed Wed May 31 11:06:30 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-chr1 49721616 49821616
-chr1 95059425 95159425
-chr1 207236313 207336313
-chr2 73790843 73890843
-chr3 134465321 134565321
-chr4 43433669 43533669
-chr4 122032777 122132777
-chr5 12701747 12801747
-chr5 58501529 58601529
-chr5 152853250 152953250
-chr6 136085023 136185023
-chr6 147019529 147119529
-chr7 14192964 14292964
-chr7 125519883 125619883
-chr8 77652872 77752872
-chr8 108375665 108475665
-chr9 2984971 3084971
-chr10 978822 1078822
-chr11 18395046 18495046
-chr12 47273592 47373592
-chr12 60095778 60195778
-chr12 84854096 84954096
-chr12 95157539 95257539
-chr14 23982000 24082000
-chr16 1875335 1975335
-chr16 66789863 66889863
-chr18 64644131 64744131
-chr21 15966609 16066609
diff -r 81faa1567178 -r 565118df598a iwtomics/example/Feature1.bed
--- a/iwtomics/example/Feature1.bed Wed May 31 11:06:30 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,5400 +0,0 @@
-chr1 91399892 91401892 0.914729028492568
-chr1 91401892 91403892 1.03788669317729
-chr1 91403892 91405892 1.15695078809331
-chr1 91405892 91407892 1.05433971377051
-chr1 91407892 91409892 1.05827244724317
-chr1 91409892 91411892 1.00216117481117
-chr1 91411892 91413892 0.873489001753337
-chr1 91413892 91415892 0.873100412116323
-chr1 91415892 91417892 0.928712683217515
-chr1 91417892 91419892 0.94132562114723
-chr1 91419892 91421892 1.06739894033636
-chr1 91421892 91423892 0.909275169317382
-chr1 91423892 91425892 1.10093887463398
-chr1 91425892 91427892 1.05342912580018
-chr1 91427892 91429892 0.970074712768588
-chr1 91429892 91431892 0.742552329847752
-chr1 91431892 91433892 1.09649292566553
-chr1 91433892 91435892 0.902578291528885
-chr1 91435892 91437892 0.821718064516058
-chr1 91437892 91439892 0.909063175846949
-chr1 91439892 91441892 1.12598647717153
-chr1 91441892 91443892 0.962991989888592
-chr1 91443892 91445892 0.886361985680751
-chr1 91445892 91447892 1.19735794895968
-chr1 91447892 91449892 1.1058589065373
-chr1 91449892 91451892 1.11830938343819
-chr1 91451892 91453892 0.891849450289035
-chr1 91453892 91455892 0.921613352575372
-chr1 91455892 91457892 0.961394603438276
-chr1 91457892 91459892 0.942120540462845
-chr1 91459892 91461892 1.04179227745858
-chr1 91461892 91463892 0.846036296260439
-chr1 91463892 91465892 0.903782108017989
-chr1 91465892 91467892 0.926324469715607
-chr1 91467892 91469892 1.01617788108211
-chr1 91469892 91471892 1.01871994841433
-chr1 91471892 91473892 0.86346600407464
-chr1 91473892 91475892 0.911534382002842
-chr1 91475892 91477892 0.909397860657818
-chr1 91477892 91479892 0.882437981483481
-chr1 91479892 91481892 1.20022730271379
-chr1 91481892 91483892 1.02286707465404
-chr1 91483892 91485892 1.00824959158441
-chr1 91485892 91487892 1.13387236604912
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diff -r 81faa1567178 -r 565118df598a iwtomics/example/Feature2.bed
--- a/iwtomics/example/Feature2.bed Wed May 31 11:06:30 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 81faa1567178 -r 565118df598a iwtomics/example/features.header.bed.txt
--- a/iwtomics/example/features.header.bed.txt Wed May 31 11:06:30 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-Feature1.bed ftr1 Feature 1
-Feature2.bed ftr2 Feature 2
\ No newline at end of file
diff -r 81faa1567178 -r 565118df598a iwtomics/example/regions.header.txt
--- a/iwtomics/example/regions.header.txt Wed May 31 11:06:30 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-Elements1_regions.bed elem1 Elements 1
-Elements2_regions.bed elem2 Elements 2
-Elements3_regions.bed elem3 Elements 3
-Controls_regions.bed control Controls
\ No newline at end of file
diff -r 81faa1567178 -r 565118df598a loadandplot.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/loadandplot.R Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,146 @@
+if (require("IWTomics",character.only = TRUE,quietly = FALSE)) {
+ require(tools,quietly = FALSE)
+ args=commandArgs(TRUE)
+
+ for (i in seq_along(args)) {
+ message(args[[i]])
+ }
+
+ # get args names and values
+ args_values=strsplit(args,'=')
+ args_names=unlist(lapply(args_values,function(arg) arg[1]))
+ names(args_values)=args_names
+ args_values=lapply(args_values,function(arg) arg[2])
+ # read filenames
+ outrdata=args_values$outrdata
+ outregions=args_values$outregions
+ outfeatures=args_values$outfeatures
+ outpdf=args_values$outpdf
+ regionspaths=unlist(strsplit(args_values$regionspaths,'\\|'))
+ if("regionsheaderfile" %in% args_names){
+ # the file regionsheaderfile must contain as first column the (unique) regionsfilenames,
+ # as second column the corresponding ids and as third column the names
+ tryCatch({
+ regionsheader=read.delim(args_values$regionsheaderfile,header=FALSE,stringsAsFactors=FALSE,row.names=1,sep="\t")
+ regionsfilenames=unlist(strsplit(args_values$regionsfilenames,'\\|'))
+ if(length(setdiff(regionsfilenames,row.names(regionsheader)))) {
+ quit(save="no", status=11)
+ stop('Not all regionsfilenames are present in the first column of regionsheader.')
+ }
+ id_regions=regionsheader[regionsfilenames,1]
+ name_regions=regionsheader[regionsfilenames,2]
+ }, error = function(err) {
+ quit(save="no", status=10) #error on header file
+ stop(err)
+ })
+ }else{
+ eval(parse(text=args[[which(args_names=='regionsgalaxyids')]]))
+ id_regions=paste0('data_',regionsgalaxyids)
+ name_regions=paste0('data_',regionsgalaxyids)
+ }
+ featurespaths=unlist(strsplit(args_values$featurespaths,'\\|'))
+ if("featuresheaderfile" %in% args_names){
+ # the file featuresheaderfile must contain as first column the (unique) featuresfilenames,
+ # as second column the corresponding ids and as third column the names
+ tryCatch({
+ featuresheader=read.delim(args_values$featuresheaderfile,header=FALSE,stringsAsFactors=FALSE,row.names=1,sep="\t")
+ featuresfilenames=unlist(strsplit(args_values$featuresfilenames,'\\|'))
+ if(length(setdiff(featuresfilenames,row.names(featuresheader)))) {
+ quit(save="no", status=21)
+ stop('Not all featuresfilenames are present in the first column of featuresheader.')
+ }
+ id_features=featuresheader[featuresfilenames,1]
+ name_features=featuresheader[featuresfilenames,2]
+ }, error = function(err) {
+ quit(save="no", status=20) #error on header file
+ stop(err)
+ })
+ }else{
+ eval(parse(text=args[[which(args_names=='featuresgalaxyids')]]))
+ id_features=paste0('data_',featuresgalaxyids)
+ name_features=paste0('data_',featuresgalaxyids)
+ }
+ # read parameters (from smoothing on)
+ i_smoothing=which(args_names=='smoothing')
+ for(i in i_smoothing:length(args)){
+ eval(parse(text=args[[i]]))
+ }
+
+ # load data
+ tryCatch({
+ regionsFeatures=IWTomicsData(regionspaths,featurespaths,alignment,
+ id_regions,name_regions,id_features,name_features,start.are.0based=start.are.0based)
+ }, error = function(err) {
+ if(grepl('invalid format',err$message)){
+ quit(save="no", status=31) # error, not enough columns in input file
+ }else if(grepl('duplicated regions',err$message)){
+ quit(save="no", status=32) # error, duplicated regions in region file
+ }else if(grepl('duplicated windows',err$message)){
+ quit(save="no", status=33) # error, duplicated windows in feature file
+ }else if(grepl('overlapping windows',err$message)){
+ quit(save="no", status=34) # error, overlapping windows in feature file
+ }else if(grepl('not all regions in datasets',err$message)){
+ quit(save="no", status=35) # error, windows in feature files do not cover all regions in region files
+ }else if(grepl('ifferent size windows',err$message)){
+ quit(save="no", status=36) # error, all windows in a feature files must have the same size
+ }
+ #error loading data
+
+ stop(err)
+
+ quit(save="no", status=30)
+
+ })
+
+ # smooth data
+ if(smoothing!='no'){
+ tryCatch({
+ if(smoothing=='locpoly'){
+ dist_knots=10
+ }else if(smoothing=='kernel'){
+ degree=3
+ dist_knots=10
+ }else if(smoothing=='splines'){
+ bandwidth=5
+ }
+ if(alignment=='scale'){
+ if(scale==0){
+ regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps,
+ bandwidth=bandwidth,degree=degree,dist_knots=dist_knots)
+ }else{
+ regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps,
+ bandwidth=bandwidth,degree=degree,dist_knots=dist_knots,scale_grid=scale)
+ }
+ }else{
+ regionsFeatures=smooth(regionsFeatures,type=smoothing,fill_gaps=fill_gaps,
+ bandwidth=bandwidth,degree=degree,dist_knots=dist_knots)
+ }
+ }, error = function(err) {
+ quit(save="no", status=40) #error on smoothing
+ stop(err)
+ })
+ }
+
+ # plot data
+ pdf(outpdf,width=10,height=8)
+ if(plottype=='boxplot'){
+ # fix repeated probs
+ probs=sort(unique(probs))
+ }else{
+ probs=c(0.25,0.5,0.75)
+ }
+ plot(regionsFeatures,type=plottype,probs=probs,average=average,size=size,ask=FALSE)
+ dev.off()
+
+ # create output
+ #write.table(cbind(unlist(strsplit(args_values$regionsfilenames,'\\|')),idRegions(regionsFeatures),nameRegions(regionsFeatures)),
+ #file=outregions,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+ write.table(as.data.frame(t(idRegions(regionsFeatures))),file=outregions,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+ #write.table(cbind(unlist(strsplit(args_values$featuresfilenames,'\\|')),idFeatures(regionsFeatures),nameFeatures(regionsFeatures)),
+ #file=outfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+ write.table(as.data.frame(t(idFeatures(regionsFeatures))),file=outfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+ save(regionsFeatures,file=outrdata)
+}else{
+ quit(save="no", status=255)
+ stop("Missing IWTomics package")
+}
\ No newline at end of file
diff -r 81faa1567178 -r 565118df598a loadandplot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/loadandplot.xml Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,325 @@
+
+ Smooth and Plot
+
+ macros.xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+& /dev/null
+]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+This tool imports a collection of genomic region datasets, and associates to each region
+multiple genomic feature measurements. It allows to align the regions in multiple ways
+(center, left, right or scale alignment), to smooth the feature curves (possibly filling gaps in the
+measurements) and to create a graphical representation of the feature measurements in each
+region datasets (aligned curves or pointwise quantile curves).
+
+-----
+
+**Region datasets**
+
+Each region dataset can be provided as a BED or Tabular file with tab delimited columns chr
+start end (extra columns present in the input file are ignored). Regions can be of different
+length::
+
+ chr2 49960150 50060150
+ chr2 55912445 56012445
+ ...
+
+-----
+
+**Feature measurements**
+
+Feature measurements corresponding to all the regions can be provided as a BED or Tabular
+file with tab delimited columns chr start end value::
+
+ chr2 49960150 49962150 0.9426
+ chr2 49962150 49964150 0.7816
+ ...
+
+Each feature must be measured in windows of a fixed size inside all the regions (missing
+values must be indicated as NA). Another way to import feature measurements is from a
+Tabular file with the first three columns chr start end corresponding to the different genomic
+regions, followed on the same row by all the measurements in fixed-size windows::
+
+ chr2 49960150 50060150 0.9426 0.7816 0.8921 ... ... 1.2063
+ chr2 55912445 56012445 0.8719 0.9975 1.1619 ... ... 0.9601
+ ...
+
+-----
+
+**Output**
+
+The tool returns:
+
+1. RData with the IWTomicsData object, that stores the aligned genomic region datasets, and their associated feature measurements;
+2. Region dataset identifiers;
+3. Feature identifiers;
+4. PDF file with the plotted data.
+
+1-3 can be used as input of the tool *IWTomics Test and Plot*
+
+-----
+
+.. class:: infomark
+
+**Notes**
+
+This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy) and Marzia A. Cremona (The Pennsylvania State University, USA).
+
+It implements a simplified version of the methods *smooth* and *plot* for *IWTomicsData* objects.
+The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
+
+.. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
+
+
+
+
+ @ARTICLE{
+ iwt-functional-data,
+ author = {Pini, Alessia and Vantini, Simone},
+ title = {Interval-Wise Testing for functional data},
+ journal = {Journal of Nonparametric Statistics},
+ year = {2017},
+ volume = {29},
+ number = {2},
+ pages = {407-424}
+ }
+
+
+ @MANUAL{
+ iwtomics,
+ author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
+ title = {IWTomics: Interval-Wise Testing for Omics Data},
+ note = {R package version 0.99.12},
+ year = {2017}
+ }
+
+
+
+
diff -r 81faa1567178 -r 565118df598a macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,9 @@
+
+ 1.0.0
+
+
+ R
+ bioconductor-iwtomics
+
+
+
\ No newline at end of file
diff -r 81faa1567178 -r 565118df598a plotwithscale.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/plotwithscale.R Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,117 @@
+if (require("IWTomics",character.only = TRUE,quietly = FALSE)) {
+ args=commandArgs(TRUE)
+
+ # get args names and values
+ args_values=strsplit(args,'=')
+ args_names=unlist(lapply(args_values,function(arg) arg[1]))
+ names(args_values)=args_names
+ args_values=lapply(args_values,function(arg) arg[2])
+ # read filenames
+ adjustedpvalue=args_values$adjustedpvalue
+ iwtomicsrespdf=args_values$iwtomicsrespdf
+ iwtomicssumpdf=args_values$iwtomicssumpdf
+ iwtomicsrdata=args_values$iwtomicsrdata
+ iwtomicstests=args_values$iwtomicstests
+ iwtomicsselectedfeatures=args_values$iwtomicsselectedfeatures
+ test_subset=paste0('c(',strsplit(args_values$test_subset,'\\|')[[1]],')')
+ feature_subset=paste0('c(',strsplit(args_values$feature_subset,'\\|')[[1]],')')
+ # read parameters (from test_subset on)
+ i_scale_subset=which(args_names=='scale_subset')
+ for(i in i_scale_subset:length(args)){
+ eval(parse(text=args[[i]]))
+ }
+
+ # load RData
+ load(iwtomicsrdata)
+ # read testids and featureids and check them
+ unlisted=lapply(seq_along(test_subset),
+ function(i){
+ test_subset_i=eval(parse(text=test_subset[i]))
+ feature_subset_i=eval(parse(text=feature_subset[i]))
+ test_subset_i=rep(test_subset_i,each=length(feature_subset_i))
+ feature_subset_i=rep(feature_subset_i,length.out=length(test_subset_i))
+ scale_subset_i=rep(scale_subset[i],length(test_subset_i))
+ return(list(test_subset=test_subset_i,feature_subset=feature_subset_i,scale_subset=scale_subset_i))
+ })
+ test_subset=unlist(lapply(unlisted,function(l) l$test_subset))
+ feature_subset=unlist(lapply(unlisted,function(l) l$feature_subset))
+ scale_subset=unlist(lapply(unlisted,function(l) l$scale_subset))
+ testids=as.character(read.delim(iwtomicstests,header=FALSE,sep='\t',stringsAsFactors=FALSE))
+ featureids=as.character(read.delim(iwtomicsselectedfeatures,header=FALSE,sep='\t',stringsAsFactors=FALSE))
+ id_features_subset=featureids[feature_subset]
+ if(sum(testids!=paste(testInput(regionsFeatures_test)$id_region1,'vs',testInput(regionsFeatures_test)$id_region2))){
+ quit(save="no", status=10)
+ stop('Wrong test ids')
+ }
+ if(sum(featureids!=idFeatures(regionsFeatures_test))){
+ quit(save="no", status=20)
+ stop('Wrong feature ids')
+ }
+ # retrieve test and features_subset ids
+ id_features_subset=featureids[feature_subset]
+ if(sum(duplicated(paste0(test_subset,id_features_subset)))){
+ quit(save="no", status=30)
+ stop('Two scale thresholds selected for the same test and feature.')
+ }
+ # If scale_subset=0, do not change the threshold
+ default=(scale_subset==0)
+ scale_subset=scale_subset[!default]
+ test_subset=test_subset[!default]
+ id_features_subset=id_features_subset[!default]
+
+ # get scale threshold
+ scale_threshold=lapply(regionsFeatures_test@test$result,
+ function(result) unlist(lapply(result,function(feature) feature$max_scale)))
+ for(i in seq_along(test_subset)){
+ if(scale_threshold[[test_subset[i]]][id_features_subset[i]]
+ on Test Scale
+
+ macros.xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+& /dev/null
+]]>
+
+
+
+
+
+ ...
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+This tool allows to select the scale for the Interval-Wise Testing results. In particular, it returns the p-value curves
+for the different tests performed at the selected scale, and it creates a graphical representation of the
+Interval-Wise Testing results and a summary plot (optional) at the selected scale.
+
+-----
+
+**Input files**
+
+RData file with the IWTomicsData object with test results, tabular files with test IDs and feature IDs.
+These files are created by the tool *IWTomics Test and Plot*.
+
+-----
+
+**Output**
+
+The tool returns:
+
+1. TXT file with an adjusted p-value curve for every test performed at the selected scale;
+2. PDF file with the plotted test results;
+3. PDF file with the summary plot.
+
+-----
+
+.. class:: infomark
+
+**Notes**
+
+This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy) and Marzia A. Cremona (The Pennsylvania State University, USA).
+
+It implements a simplified version of the function *IWTomicsTest*, *plotTest* and *plotSummary* for *IWTomicsData* objects.
+The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
+
+.. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
+
+
+
+
+ @ARTICLE{
+ iwt-functional-data,
+ author = {A Pini and S. Vantini},
+ title = {Interval-Wise Testing for functional data},
+ journal = {Journal of Nonparametric Statistics},
+ year = {2017},
+ volume = {29},
+ number = {2},
+ pages = {407-424}
+ }
+
+
+ @MANUAL{
+ iwtomics,
+ author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
+ title = {IWTomics: Interval-Wise Testing for Omics Data},
+ note = {R package version 0.99.12},
+ year = {2017}
+ }
+
+
+
+
diff -r 81faa1567178 -r 565118df598a testandplot.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/testandplot.R Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,99 @@
+if (require("IWTomics",character.only = TRUE,quietly = FALSE)) {
+ args=commandArgs(TRUE)
+
+ # get args names and values
+ args_values=strsplit(args,'=')
+ args_names=unlist(lapply(args_values,function(arg) arg[1]))
+ names(args_values)=args_names
+ args_values=lapply(args_values,function(arg) arg[2])
+ # read filenames
+ adjustedpvaluematrix=args_values$adjustedpvaluematrix
+ iwtomicsrespdf=args_values$iwtomicsrespdf
+ iwtomicssumpdf=args_values$iwtomicssumpdf
+ regionids=args_values$regionids
+ featureids=args_values$featureids
+ rdatafile=args_values$rdatafile
+ iwtomicsrdata=args_values$iwtomicsrdata
+ iwtomicstests=args_values$iwtomicstests
+ iwtomicsselectedfeatures=args_values$iwtomicsselectedfeatures
+ # read parameters (from region1 on)
+ i_region1=which(args_names=='region1')
+ for(i in i_region1:length(args)){
+ eval(parse(text=args[[i]]))
+ }
+
+ # load RData
+ load(rdatafile)
+ # read regionids and featureids
+ regionids=as.character(read.delim(regionids,header=FALSE,sep='\t',stringsAsFactors=FALSE))
+ featureids=as.character(read.delim(featureids,header=FALSE,sep='\t',stringsAsFactors=FALSE))
+ # retrieve region1, region2 and features_subset ids and check they are in the RData
+ id_region1=regionids[region1]
+ id_region2=regionids[region2]
+ id_features_subset=featureids[features_subset]
+ if(length(setdiff(c(id_region1,id_region2),idRegions(regionsFeatures)))!=0){
+ quit(save="no", status=10)
+ stop('Wrong region ids')
+ }
+ if(length(setdiff(id_features_subset,idFeatures(regionsFeatures)))!=0){
+ quit(save="no", status=20)
+ stop('Wrong feature ids')
+ }
+ if(sum(duplicated(paste0(id_region1,id_region2)))){
+ quit(save="no", status=30)
+ stop('Same test repeated multiple times.')
+ }
+
+ # perform test
+ tryCatch({
+ # fix repeated probs
+ if(statistics=='quantile'){
+ # fix repeated probs
+ testprobs=sort(unique(testprobs))
+ }else{
+ testprobs=0.5
+ }
+ regionsFeatures_test=IWTomicsTest(regionsFeatures,id_region1,id_region2,id_features_subset,
+ statistics=statistics,probs=testprobs,B=B)
+ # create adjustedvaluematrix output
+ for(test in seq_along(id_region1)){
+ for(id_feature in id_features_subset){
+ write(paste0('Test: ',id_region1[test],' vs ',id_region2[test],', on feature ',id_feature),
+ file=adjustedpvaluematrix,append=TRUE,sep='\t')
+ pval=regionsFeatures_test@test$result[[test]][[id_feature]]$adjusted_pval_matrix
+ row.names(pval)=paste('Scale',rev(seq_len(nrow(pval))))
+ write.table(pval,file=adjustedpvaluematrix,append=TRUE,sep='\t',quote=FALSE,row.names=TRUE,col.names=FALSE)
+ write('',file=adjustedpvaluematrix,append=TRUE,sep='\t')
+ }
+ }
+ }, error = function(err) {
+ quit(save="no", status=40) #error testing
+ stop(err)
+ })
+
+ # plot test results
+ pdf(iwtomicsrespdf,width=5,height=7)
+ if(plottype=='boxplot'){
+ # fix repeated probs
+ probs=sort(unique(probs))
+ }else{
+ probs=c(0.25,0.5,0.75)
+ }
+ plotTest(regionsFeatures_test,alpha=testalpha,type=plottype,probs=probs,average=average,size=size,ask=FALSE)
+ dev.off()
+
+ # plot summary results
+ if(groupby!='none'){
+ pdf(iwtomicssumpdf,width=15,height=10)
+ plotSummary(regionsFeatures_test,alpha=summaryalpha,only_significant=only_significant,groupby=groupby,ask=FALSE,append=TRUE)
+ dev.off()
+ }
+
+ # create output
+ write.table(as.data.frame(t(paste(id_region1,'vs',id_region2))),file=iwtomicstests,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+ write.table(as.data.frame(t(idFeatures(regionsFeatures_test))),file=iwtomicsselectedfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
+ save(regionsFeatures_test,file=iwtomicsrdata)
+}else{
+ quit(save="no", status=255)
+ stop("Missing IWTomics package")
+}
\ No newline at end of file
diff -r 81faa1567178 -r 565118df598a testandplot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/testandplot.xml Wed May 31 11:07:22 2017 -0400
@@ -0,0 +1,239 @@
+
+ and Plot
+
+ macros.xml
+
+
+
+
+
+
+
+
+
+
+
+
+& /dev/null
+]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+This tool statistically evaluates differences in genomic features between groups of regions along the genome.
+In particular, it implements the Interval-Wise Testing for omics data, an extended version of the Interval-Wise
+Testing for functional data presented in Pini and Vantini (2017). It allows to perform multiple two sample permutation
+tests between pairs of region datasets, on several features. It returns the adjusted p-value curves for every test
+and all possible scales. Moreover, it creates a graphical representation of the Interval-Wise Testing results
+and a summary plot (optional) with p-values at the maximum scale. The tool *IWTomics Plot with Threshold on Test Scale*
+permits to select the scale to be used in the plots.
+
+-----
+
+**Input files**
+
+RData file with the IWTomicsData object, tabular files with region dataset IDs and feature IDs.
+These files are created by the tool *IWTomics Load Smooth and Plot*.
+
+-----
+
+**Output**
+
+The tool returns:
+
+1. TXT file with an adjusted p-value matrix for every test performed. Each matrix contains a p-value curve (row) for every scale considered in the test;
+2. PDF file with the plotted test results;
+3. PDF file with the summary plot;
+4. RData with the IWTomicsData object with the test results;
+5. Test identifiers;
+6. Feature identifiers.
+
+4-6 can be used as input of the tool *IWTomics Plot with Threshold on Test Scale*
+
+-----
+
+.. class:: infomark
+
+**Notes**
+
+This Galaxy tool has been developed by Fabio Cumbo (Third University of Rome, Italy) and Marzia A. Cremona (The Pennsylvania State University, USA).
+
+It implements a simplified version of the function *IWTomicsTest*, *plotTest* and *plotSummary* for *IWTomicsData* objects.
+The complete version can be found in the *R/Bioconductor* package *IWTomics* (see vignette_).
+
+.. _vignette: https://bioconductor.org/packages/release/bioc/vignettes/IWTomics/inst/doc/IWTomics.pdf
+
+
+
+
+ @ARTICLE{
+ iwt-functional-data,
+ author = {A Pini and S. Vantini},
+ title = {Interval-Wise Testing for functional data},
+ journal = {Journal of Nonparametric Statistics},
+ year = {2017},
+ volume = {29},
+ number = {2},
+ pages = {407-424}
+ }
+
+
+ @MANUAL{
+ iwtomics,
+ author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone},
+ title = {IWTomics: Interval-Wise Testing for Omics Data},
+ note = {R package version 0.99.12},
+ year = {2017}
+ }
+
+
+
+