{% for mapping_method in dataset.group.mapping_names %}
{% if mapping_method == "GEMMA" %}
{% if genofiles and genofiles|length>0 %}
{% endif %}
{% elif mapping_method == "QTLReaper" %}
{% if genofiles and genofiles|length>0 %}
{% else %}
{% endif %}
{% elif mapping_method == "R/qtl" %}
{% if genofiles and genofiles|length > 0 %}
{% else %}
{% endif %}
{% if sample_groups[0].attributes|length > 0 %}
{% endif %}
{% if genofiles and genofiles|length > 0 %}
{% endif %}
{% endif %}
{% endfor %}
{% 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 the near future—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.
{% else %}
Mapping options are disabled for data not matched with genotypes.
{% endif %}