From 12b7eebfc1190616d1bb378eb425faeda2951412 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 14 Aug 2019 17:17:38 -0500
Subject: removed LOD text from index page until LOD search works and cleaned
up mapping options appearance/text some
---
.../static/new/javascript/init_genome_browser.js | 2 +-
wqflask/wqflask/templates/index_page_orig.html | 6 ++---
.../templates/show_trait_mapping_tools.html | 26 ++++++++++++----------
3 files changed, 18 insertions(+), 16 deletions(-)
diff --git a/wqflask/wqflask/static/new/javascript/init_genome_browser.js b/wqflask/wqflask/static/new/javascript/init_genome_browser.js
index a544f3cb..6a19fe08 100644
--- a/wqflask/wqflask/static/new/javascript/init_genome_browser.js
+++ b/wqflask/wqflask/static/new/javascript/init_genome_browser.js
@@ -17,7 +17,7 @@ var legendWidth = 140.0;
if ('significant' in js_data) {
var significant_score = parseFloat(js_data.significant)
} else {
- var significant_score = 4
+ var significant_score = js_data.max_score * 0.75
}
var score = { min: 0.0, max: js_data.max_score, sig: significant_score };
var gwasPadding = { top: 35.0,
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index bdf51bf8..3b008d83 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -150,14 +150,14 @@
RANGE=(1.5 2.5) in the Any field finds traits with values with a specified fold-range (minimum = 1).
Useful for finding "housekeeping genes" (1.0 1.2) or highly variable molecular assays (10 100).
-
LRS=(15 1000) or LOD=(2 8) finds all traits with peak LRS or LOD scores between lower and upper limits.
+
LRS=(15 1000) finds all traits with peak LRS scores between lower and upper limits.
LRS=(9 999 Chr4 122 155) finds all traits on Chr 4 from 122 and 155 Mb with LRS scores between 9 and 999.
-
cisLRS=(15 1000 5) or cisLOD=(2 8 5) finds all cis eQTLs with peak LRS or LOD scores between lower and upper limits,
+
cisLRS=(15 1000 5) finds all cis eQTLs with peak LRS scores between lower and upper limits,
with an inclusion zone of 5 Mb around the parent gene.
-
transLRS=(15 1000 5) or transLOD=(2 8 5) finds all trans eQTLs with peak LRS or LOD scores between lower and upper limits,
+
transLRS=(15 1000 5) finds all trans eQTLs with peak LRS scores between lower and upper limits,
with an exclusion zone of 5 Mb around the parent gene.
{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
-
+
{% else %}
-
+
{% endif %}
+ Yes No
+
@@ -202,14 +205,14 @@
-->
-
+
@@ -351,15 +354,14 @@
-
+
GEMMA
GEMMA is software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model for genome-wide association studies (GWAS).
{% if dataset.group.mapping_id == "1" %}
-
Interval Mapping
-
Interval mapping is a process in which the statistical significance of a hypothetical QTL is evaluated at regular points across a chromosome, even in the absence of explicit genotype data at those points.
- The default option is a version of qtlrearper rewritten in RUST that should fix some of the issues the original had. You can still use the original with the Version option.
- Please let us know if you encounter any issues while using the new version.
+
Haley-Knott Regression
+
This method is implementing using the tool QTLReaper. Interval mapping (the last option) is a process in which the statistical significance of a hypothetical QTL is evaluated at regular points across a chromosome, even in the absence of explicit genotype data at those points.
+ The default option is a version of QTLReaper rewritten in RUST that should fix some of the issues the original had. You can still use the original with the Version option.
R/qtl
R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses.