# R interface for TASSEL's association methods

Source:`R/analysis_association_functions.R`

`assocModelFitter.Rd`

This function acts as a front-end for TASSEL's extensive association analysis methods. Using this function, users can run the following TASSEL association methods:

best linear unbiased estimates (BLUEs)

generalized linear model (GLM)

mixed linear model

Fast association (Shabalin 2012)

## Usage

```
assocModelFitter(
tasObj,
formula,
fitMarkers = FALSE,
kinship = NULL,
fastAssociation = FALSE,
maxP = 0.001,
maxThreads = NULL,
minClassSize = 0,
outputFile = NULL,
biallelicOnly = FALSE,
appendAddDom = FALSE
)
```

## Arguments

- tasObj
An object of class

`TasselGenotypePenotype`

.- formula
An R-based linear model formula. The general layout of this formula uses the following TASSEL data scheme:

`<data> ~ <factor> and/or <covariate>`

. If all traits in a Phenotype object should be ran, a simplified formula (`. ~ .`

) can be used. This scheme can also be used for running all`<data>`

or`<factor>`

and/or`<covariate>`

data as well. Single variables are separated witha`+`

operator. See vignette for further clarification.- fitMarkers
Should marker data be fitted? If

`TRUE`

, GLM analysis will be executed. If`FALSE`

, BLUEs will be calculated. Defaults to`FALSE`

.- kinship
Should kinship data be accounted for in the model? If so, a TASSEL kinship matrix object of class

`TasselDistanceMatrix`

must be submitted. Defaults to`NULL`

.- fastAssociation
Should TASSEL's Fast Association plugin be used? Consider setting to

`TRUE`

if you have many phenotypes in your data set.- maxP
Maximum p-value (0 - 1) to be reported. Currently works with fast association only. Defaults to a p-value of

`0.001`

will be used as a threshold.**Note:**p-value parameter will not be used for BLUE analysis.- maxThreads
Maximum threads to be used when running fast association. If

`NULL`

, all threads on machine will be used.- minClassSize
The minimum acceptable genotype class size. Genotypes in a class with a smaller size will be set to missing. Defaults to 0.

- outputFile
Output file prefix to be specified in case you want to write data directly to disk. Highly recommended for large datasets. If

`NULL`

, no data will be saved to disk. If a character- biallelicOnly
Only test sites that are bi-allelic. The alternative is to test sites with two or more alleles. Defaults to

`FALSE`

- appendAddDom
If true, additive and dominance effect estimates will be added to the stats report for bi-allelic sites only. The effect will only be estimated when the data source is genotype (not a probability). The additive effect will always be non-negative. Defaults to

`FALSE`

.