assocModelFitter: R interface for TASSEL's association methods
In maize-genetics/rTASSEL: R Front-End for TASSEL

View source: R/analysis_association_functions.R

assocModelFitter

R Documentation

R interface for TASSEL's association methods

Description

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`.