+ {% if sample_groups[0].attributes|length > 0 %}
+
+
+
+
+
+
+
+ {% endif %}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ {% if g.user_session.num_collections < 1 %}
+ No collections available. Please add traits to a collection to use them as covariates.
+ {% else %}
+
+
+
+
+
+ {% endif %}
+
+
+
+
+
+
+
+
+
+
{% endif %}
{% endfor %}
@@ -345,8 +452,10 @@
GEMMA
Maps traits with correction for kinship among samples using a linear mixed model method, and also allows users to fit multiple covariates such as sex, age, treatment, and genetic markers (PMID: 2453419, and GitHub code). GEMMA incorporates the Leave One Chromosome Out (LOCO) method to ensure that the correction for kinship does not remove useful genetic variance near each marker. Markers can be filtered to include only those with minor allele frequencies (MAF) above a threshold. The default MAF is 0.05.
{% elif mapping_method == "R/qtl" %}
-
R/qtl (version 1.44.9
+
R/qtl (version 1.44.9)
The original R/qtl mapping package that supports classic experimental crosses including 4-parent F2 intercrosses (e.g., NIA ITP UM-HET3). R/qtl is ideal for populations that do not have complex kinship or admixture (PMID: 12724300). Both R/qtl as implemented here, and R/qtl2 (PMID: 30591514) are available as R suites.
+
Pair Scan
+
Pair Scan using the R/qtl scantwo function.
{% elif mapping_method == "QTLReaper" %}
Haley-Knott Regression
Fast linear mapping method (PMID 16718932) works well with F2 intercrosses and backcrosses, but that is not recommended for complex or admixed populations (e.g., GWAS or heterogeneous stock studies) or for advanced intercrosses, recombinant inbred families, or diallel crosses. Interactive plots in GeneNetwork have relied on the fast HK mapping for two decades and we still use this method for mapping omics data sets and computing genome-wide permutation threshold (QTL Reaper code).