Genetics

Click on a subcategory to reveal individual genetics processes.

Subcategory	Contains processes for...	Input data requirement1Following the import of data (an {link}{Emphasis}Experimental Design File (EDF) is sometimes required), {link}{Emphasis}Tall and Wide Data Sets (which are {link}{Emphasis}SAS Data Sets) are the most common primary {link}{Emphasis}Input Data Sets required throughout JMP Genomics. Less common are stacked, square, and other specialized varieties. (See {link}{Emphasis}Other Types of Data Sets.) In many cases, an additional {link}{Emphasis}Experimental Design Data Set (EDDS), {link}{Emphasis}Annotation Data Set, or settings file is either specifiable or required. See {link}{Emphasis}Data Sets Used in JMP Genomics Processes and the documentation for individual processes for additional information.See the {link}{Emphasis}JMP Genomics Starter main page for other process categories.
Genetics Utilities	Checking and manipulation of data to improve suitability for subsequent analyses.	A wide or annotation data set, or both, depending on the process. Note: SNP Power does not require an input data set.
Relatedness Measures	Computation of kinship, relationship, identity, and population statistics.	Wide, tall, or square data, depending on the process.
Genetic Marker Statistics	Summarizing and displaying genetic marker information.	Wide data.
GWAS Testing	Genome-wide association studies analysis.	Wide data (for most).
Other Association Testing	Association tests that are not conducted at the genome level.	Wide data, with an annotation data set either optional or required, for most.
Haplotype Analysis	Estimation of unobserved haplotype frequencies, determination of haplotype from potential trait-influencing markers, and elucidation of markers determinate of haplotype diversity.	Some are specialized. See individual process descriptions.
Model-free Linkage	Sib-pair chi-square linkage tests.	A specialized identical-by-descent (IBD) data set and either a pedigree or an annotation data set, depending on the process.
Linkage Maps and QTL	Construction and viewing of linkage maps, quantitative trait loci signal detection, construction of genotype probability data sets, and generation of interval mapping models.	Either an input cross file or the output file from another process in this subcategory. Some also require an annotation data set.
Breeding Analysis	Summarizing and displaying categorical and quantitative population phenotypes; analysis of multi-environment trial (MET) genotype-by-environment interaction.	Wide or tall data, depending on the process.