From 204a308be0f741726b9a620d88fbc22b22124c81 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Fri, 29 Dec 2023 18:55:37 +0000 Subject: Namespace all modules under gn2. We move all modules under a gn2 directory. This is important for "correct" packaging and deployment as a Guix service. --- .../templates/show_trait_mapping_tools.html | 436 +++++++++++++++++++++ 1 file changed, 436 insertions(+) create mode 100755 gn2/wqflask/templates/show_trait_mapping_tools.html (limited to 'gn2/wqflask/templates/show_trait_mapping_tools.html') diff --git a/gn2/wqflask/templates/show_trait_mapping_tools.html b/gn2/wqflask/templates/show_trait_mapping_tools.html new file mode 100755 index 00000000..f1ed8922 --- /dev/null +++ b/gn2/wqflask/templates/show_trait_mapping_tools.html @@ -0,0 +1,436 @@ +
+ {% if dataset.group.mapping_names|length > 0 %} +
+
+ +
    + {% for mapping_method in dataset.group.mapping_names %} + {% if mapping_method == "GEMMA" %} +
  • + GEMMA +
    • + {% elif mapping_method == "R/qtl" %} +
  • + R/qtl +
    • +
  • + Pair Scan +
    • + {% elif mapping_method == "QTLReaper" %} +
  • + Haley-Knott Regression +
    • + {% endif %} + {% endfor %} +
+ +
+ {% for mapping_method in dataset.group.mapping_names %} + {% if mapping_method == "GEMMA" %} +
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+ {% if genofiles and genofiles|length>0 %} +
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+ {% endif %} +
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+ {% elif mapping_method == "QTLReaper" %} +
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+ {% if genofiles and genofiles|length>0 %} +
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+ {% else %} +
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+ {% endif %} +
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+ {% elif mapping_method == "R/qtl" %} +
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+ {% if genofiles and genofiles|length > 0 %} +
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+ {% else %} +
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+ {% endif %} +
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+ {% if sample_groups[0].attributes|length > 0 %} +
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+ {% endif %} +
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+ {% if genofiles and genofiles|length > 0 %} +
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+ {% endif %} + {% endfor %} +
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+ {% for mapping_method in dataset.group.mapping_names %} + {% if mapping_method == "GEMMA" %} +
GEMMA
+
GEMMA maps with correction for kinship using a linear mixed model and can include covariates such as sex and age. Defaults include a minor allele frequency of 0.05 and the leave-one-chromosome-out method (PMID: 2453419, and GitHub code).
+ {% elif mapping_method == "R/qtl" %} +
R/qtl (version 1.44.9)
+
R/qtl maps using several models and uniquely support 4-way intercrosses such as the "Aging Mouse Lifespan Studies" (NIA UM-HET3). We will add support for R/qtl2 (PMID: 30591514) in 2023—a version that handles complex populations with admixture and many haplotypes.
+
Pair Scan (R/qtl v 1.44.9)
+
The Pair Scan mapping tool performs a search for joint effects of two separate loci that may influence a trait. This search typically requires large sample sizes. Pair Scans can included covariates such as age and sex. For more on this function by K. Broman and colleagues see www.rdocumentation.org/packages/qtl/versions/1.60/topics/scantwo
+ {% elif mapping_method == "QTLReaper" %} +
Haley-Knott Regression
+
HK regression (QTL Reaper) is a fast mapping method with permutation that works well with F2 intercrosses and backcrosses (PMID 16718932), but is not recommended for admixed populations, advanced intercrosses, or strain families such as the BXDs (QTL Reaper code).
+ {% endif %} + {% endfor %} +
+
+ More information on R/qtl mapping models and methods can be found here. +
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+ + {% else %} + Mapping options are disabled for data not matched with genotypes. + {% endif %} +
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