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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. IfFALSE
, BLUEs will be calculated. Defaults toFALSE
.- kinship
Should kinship data be accounted for in the model? If so, a TASSEL kinship matrix object of class
TasselDistanceMatrix
must be submitted. Defaults toNULL
.- 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
.