# rTASSEL

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`rTASSEL` is an R-based front-end for accessing key TASSEL 5 methods and
tools. This allows users to run powerful TASSEL 5 analyses within a
unified R workflow, without switching between environments. `rTASSEL`
also offers performance and feature advantages over other R packages.
See [these
benchmarks](https://maize-genetics.github.io/rTASSEL/articles/rtassel_benchmarks.html)
for details.

## Citation

To cite `rTASSEL`, please use the following citation:

> Monier et al., (2022). rTASSEL: An R interface to TASSEL for analyzing
> genomic diversity. Journal of Open Source Software, 7(76), 4530,
> <https://doi.org/10.21105/joss.04530>

## Installation

### Stable release

``` r

# install.packages("pak")
pak::pak("maize-genetics/rTASSEL@v0.13.0")
```

### Developmental version

``` r

# install.packages("pak")
pak::pak("maize-genetics/rTASSEL")
```

> **Note**
>
> Since `rTASSEL` uses `rJava`, you will need a working version of Java
> (≥ 8).
>
> **Mac/Linux users**: you may need to run `R CMD javareconf` if you run
> into issues with installing `rJava` via `pak`. More installation tips
> can be found
> [here](https://rtassel.maizegenetics.net/articles/rtassel_installation.html).
>
> **I also recommend checking out Egor Kotov’s
> [rJavaEnv](https://www.ekotov.pro/rJavaEnv/) package to further
> automate your R to Java setup!**

### Docker

To avoid configuring Java and R locally, you can build a container from
the
[`docker/Dockerfile`](https://github.com/maize-genetics/rTASSEL/blob/master/docker/Dockerfile)
in this repository. See the [installation
article](https://rtassel.maizegenetics.net/articles/rtassel_installation.html#running-from-docker)
for build instructions, `docker run` examples, and RStudio Server usage.

## Demo

If you want to test out what this package does but do not want to
install it locally, we have set up an interactive Jupyter notebook
detailing the walkthrough of `rTASSEL` on Binder. The Binder link can be
accessed through the Binder icon on this page or by clicking
[here](https://mybinder.org/v2/gh/btmonier/rTASSEL_sandbox/HEAD?labpath=getting_started.ipynb).

## Getting help

For an overview of available functions, use the following command:

    help(package = "rTASSEL")

If you need a walkthrough for potential pipelines, long-form
documentation can be found on our
[website](https://rtassel.maizegenetics.net) including a [getting
started
article](https://rtassel.maizegenetics.net/articles/rTASSEL.html).

If you would like to study a function in full, refer to the R
documentation by using `?<function>` in the console, where `<function>`
is an `rTASSEL`-based function.

# Package index

## All functions

- [`show(`*`<AssociationResults>`*`)`](https://rtassel.maizegenetics.net/reference/AssociationResults-class.md)
  : AssociationResults Class

- [`AssociationResults-validity`](https://rtassel.maizegenetics.net/reference/AssociationResults-validity.md)
  : AssociationResults validation

- [`AssociationResultsBLUE-class`](https://rtassel.maizegenetics.net/reference/AssociationResultsBLUE-class.md)
  : AssociationResultsBLUE Class

- [`AssociationResultsFast-class`](https://rtassel.maizegenetics.net/reference/AssociationResultsFast-class.md)
  : AssociationResultsFast Class

- [`AssociationResultsGLM-class`](https://rtassel.maizegenetics.net/reference/AssociationResultsGLM-class.md)
  : AssociationResultsGLM Class

- [`AssociationResultsMLM-class`](https://rtassel.maizegenetics.net/reference/AssociationResultsMLM-class.md)
  : AssociationResultsMLM Class

- [`AssociationResultsStepwise-class`](https://rtassel.maizegenetics.net/reference/AssociationResultsStepwise-class.md)
  : AssociationResultsStepwise Class

- [`show(`*`<LDRegion>`*`)`](https://rtassel.maizegenetics.net/reference/LDRegion-class.md)
  : LDRegion Class

- [`LDRegion-validity`](https://rtassel.maizegenetics.net/reference/LDRegion-validity.md)
  : LDRegion validation

- [`LDRegion()`](https://rtassel.maizegenetics.net/reference/LDRegion.md)
  : Create an LDRegion object

- [`show(`*`<LDResults>`*`)`](https://rtassel.maizegenetics.net/reference/LDResults-class.md)
  : LDResults Class

- [`LDResults-validity`](https://rtassel.maizegenetics.net/reference/LDResults-validity.md)
  : LDResults validation

- [`show(`*`<PCAResults>`*`)`](https://rtassel.maizegenetics.net/reference/PCAResults-class.md)
  : PCAResults Class

- [`PCAResults-validity`](https://rtassel.maizegenetics.net/reference/PCAResults-validity.md)
  : PCAResults validation

- [`show(`*`<TasselDistanceMatrix>`*`)`](https://rtassel.maizegenetics.net/reference/TasselDistanceMatrix-class.md)
  : TasselDistanceMatrix Class

- [`TasselGenotype-class`](https://rtassel.maizegenetics.net/reference/TasselGenotype-class.md)
  : TasselGenotype Class

- [`show(`*`<TasselGenotypePhenotype>`*`)`](https://rtassel.maizegenetics.net/reference/TasselGenotypePhenotype-class.md)
  : TasselGenotypePhenotype Class

- [`show(`*`<TasselNumericGenotype>`*`)`](https://rtassel.maizegenetics.net/reference/TasselNumericGenotype-class.md)
  : TasselNumericGenotype Class Definition

- [`TasselPhenotype-class`](https://rtassel.maizegenetics.net/reference/TasselPhenotype-class.md)
  : TasselPhenotype Class Definition

- [`as.matrix(`*`<TasselDistanceMatrix>`*`)`](https://rtassel.maizegenetics.net/reference/as.matrix.TasselDistanceMatrix.md)
  : Coerce matrix from TasselDistanceMatrix class

- [`as.matrix(`*`<TasselGenotypePhenotype>`*`)`](https://rtassel.maizegenetics.net/reference/as.matrix.TasselGenotypePhenotype.md)
  : Coerce genotype table to R matrix

- [`asTasselDistanceMatrix()`](https://rtassel.maizegenetics.net/reference/asTasselDistanceMatrix.md)
  : Coerce matrix to TasselDistanceMatrix object

- [`assocModelFitter()`](https://rtassel.maizegenetics.net/reference/assocModelFitter.md)
  : R interface for TASSEL's association methods

- [`associationType()`](https://rtassel.maizegenetics.net/reference/associationType.md)
  : Return GWAS association type

- [`attributeData()`](https://rtassel.maizegenetics.net/reference/attributeData.md)
  : Return TASSEL attribute data

- [`checkForTASSELUpdate()`](https://rtassel.maizegenetics.net/reference/checkForTASSELUpdate.md)
  : Check for a newer version of TASSEL

- [`colnames(`*`<TasselDistanceMatrix>`*`)`](https://rtassel.maizegenetics.net/reference/colnames-TasselDistanceMatrix-method.md)
  : Column names

- [`concatenate()`](https://rtassel.maizegenetics.net/reference/concatenate.md)
  : Concatenate phenotype tables

- [`createTree()`](https://rtassel.maizegenetics.net/reference/createTree.md)
  : R interface for TASSEL's tree creation methods

- [`dim(`*`<TasselDistanceMatrix>`*`)`](https://rtassel.maizegenetics.net/reference/dim-TasselDistanceMatrix-method.md)
  : Get dimensions of TasselDistanceMatrix object

- [`distanceMatrix()`](https://rtassel.maizegenetics.net/reference/distanceMatrix.md)
  : Create a TASSEL distance matrix

- [`exportGenotypeTable()`](https://rtassel.maizegenetics.net/reference/exportGenotypeTable.md)
  : Export Genotype Table to Disk

- [`filterGenotypeTableBySiteName()`](https://rtassel.maizegenetics.net/reference/filterGenotypeTableBySiteName.md)
  : Filter genotype table by site IDs

- [`filterGenotypeTableSites()`](https://rtassel.maizegenetics.net/reference/filterGenotypeTableSites.md)
  : Filter genotype table by sites

- [`filterGenotypeTableTaxa()`](https://rtassel.maizegenetics.net/reference/filterGenotypeTableTaxa.md)
  : Filter genotype table by taxa

- [`genomicPrediction()`](https://rtassel.maizegenetics.net/reference/genomicPrediction.md)
  : R interface for TASSEL's genomic prediction capabilities

- [`getPhenotypeDF()`](https://rtassel.maizegenetics.net/reference/getPhenotypeDF.md)
  :

  Get an R/`DataFrame` phenotype data frame from TASSEL object

- [`getSumExpFromGenotypeTable()`](https://rtassel.maizegenetics.net/reference/getSumExpFromGenotypeTable.md)
  : Create Summarized Experiment from a TASSEL Genotype Table

- [`imputeLDKNNi()`](https://rtassel.maizegenetics.net/reference/imputeLDKNNi.md)
  : LD KNNi imputation

- [`imputeNumeric()`](https://rtassel.maizegenetics.net/reference/imputeNumeric.md)
  : Imputation methods in Numerical Transformations

- [`intersectJoin()`](https://rtassel.maizegenetics.net/reference/intersectJoin.md)
  : Intersect join phenotype tables

- [`javaRefObj()`](https://rtassel.maizegenetics.net/reference/javaRefObj.md)
  :

  Return `rJava` reference object

- [`kinshipMatrix()`](https://rtassel.maizegenetics.net/reference/kinshipMatrix.md)
  : Create a TASSEL kinship matrix

- [`linkageDiseq()`](https://rtassel.maizegenetics.net/reference/linkageDiseq.md)
  : Calculate linkage disequilibrium from an rTASSEL genotype dataset.

- [`mds()`](https://rtassel.maizegenetics.net/reference/mds.md) :

  Run MDS on `TasselDistanceMatrix` objects

- [`mergeGenotypeTables()`](https://rtassel.maizegenetics.net/reference/mergeGenotypeTables.md)
  : Merge genotype tables

- [`ncol(`*`<TasselDistanceMatrix>`*`)`](https://rtassel.maizegenetics.net/reference/ncol-TasselDistanceMatrix-method.md)
  : Number of columns

- [`nrow(`*`<TasselDistanceMatrix>`*`)`](https://rtassel.maizegenetics.net/reference/nrow-TasselDistanceMatrix-method.md)
  : Number of rows

- [`pca()`](https://rtassel.maizegenetics.net/reference/pca.md) : Run
  PCA on Genotype Table

- [`plotLD()`](https://rtassel.maizegenetics.net/reference/plotLD.md) :
  Linkage disequilibrium plot

- [`plotManhattan()`](https://rtassel.maizegenetics.net/reference/plotManhattan.md)
  : Create a Manhattan plot from rTASSEL association output

- [`plotManhattanQC()`](https://rtassel.maizegenetics.net/reference/plotManhattanQC.md)
  : Create a QC Manhattan plots from rTASSEL association output

- [`plotPCA()`](https://rtassel.maizegenetics.net/reference/plotPCA.md)
  : Generate PCA plot

- [`plotQQ()`](https://rtassel.maizegenetics.net/reference/plotQQ.md) :
  Create a QQ plot from rTASSEL association output

- [`plotScree()`](https://rtassel.maizegenetics.net/reference/plotScree.md)
  : Generate scree plots

- [`plotSnpDensity()`](https://rtassel.maizegenetics.net/reference/plotSnpDensity.md)
  : Plot SNP density across chromosomes

- [`positionList()`](https://rtassel.maizegenetics.net/reference/positionList.md)
  : Get position list metadata from genotype table

- [`readGenotype()`](https://rtassel.maizegenetics.net/reference/readGenotype.md)
  : Read Genotype Data

- [`readGenotypePhenotype()`](https://rtassel.maizegenetics.net/reference/readGenotypePhenotype.md)
  : Wrapper function of TasselGenotypePhenotype class for
  GenotypePhenotype combined data

- [`readGenotypeTableFromGigwa()`](https://rtassel.maizegenetics.net/reference/readGenotypeTableFromGigwa.md)
  : Read genotype data from GIGWA using QBMS

- [`readGenotypeTableFromPath()`](https://rtassel.maizegenetics.net/reference/readGenotypeTableFromPath.md)
  : Wrapper function of TasselGenotypePhenotype class for genotype data

- [`readNumericGenotypeFromRMatrix()`](https://rtassel.maizegenetics.net/reference/readNumericGenotypeFromRMatrix.md)
  : Read Genotype Data from R Matrix

- [`readPhenotype()`](https://rtassel.maizegenetics.net/reference/readPhenotype.md)
  : Read and convert phenotype data into TASSEL 5 phenotype objects

- [`readPhenotypeFromDataFrame()`](https://rtassel.maizegenetics.net/reference/readPhenotypeFromDataFrame.md)
  : Wrapper function of TasselGenotypePhenotype class for phenotype data
  from an R data frame

- [`readPhenotypeFromPath()`](https://rtassel.maizegenetics.net/reference/readPhenotypeFromPath.md)
  : Wrapper function of TasselGenotypePhenotype class for phenotype data
  from a path.

- [`readTasselDistanceMatrix()`](https://rtassel.maizegenetics.net/reference/readTasselDistanceMatrix.md)
  : read TASSEL distance matrix object from file

- [`reportNames()`](https://rtassel.maizegenetics.net/reference/reportNames.md)
  [`traitNames(`*`<AssociationResults>`*`)`](https://rtassel.maizegenetics.net/reference/reportNames.md)
  : Return report names

- [`rownames(`*`<TasselDistanceMatrix>`*`)`](https://rtassel.maizegenetics.net/reference/rownames-TasselDistanceMatrix-method.md)
  : Row names

- [`seqDiversity()`](https://rtassel.maizegenetics.net/reference/seqDiversity.md)
  : Calculate sequence diversity

- [`setupTASSEL()`](https://rtassel.maizegenetics.net/reference/setupTASSEL.md)
  : Download and configure TASSEL JAR files

- [`show(`*`<TasselGenotype>`*`)`](https://rtassel.maizegenetics.net/reference/show-TasselGenotype-method.md)
  : Display TasselGenotype Object

- [`show(`*`<TasselPhenotype>`*`)`](https://rtassel.maizegenetics.net/reference/show-TasselPhenotype-method.md)
  : Display summary information of a TasselPhenotype object

- [`siteSummary()`](https://rtassel.maizegenetics.net/reference/siteSummary.md)
  : Get site summary of genotype table

- [`startLogger()`](https://rtassel.maizegenetics.net/reference/startLogger.md)
  : Start TASSEL logging information

- [`stepwiseModelFitter()`](https://rtassel.maizegenetics.net/reference/stepwiseModelFitter.md)
  : Stepwise Model Fitter

- [`tableReport()`](https://rtassel.maizegenetics.net/reference/tableReport.md)
  : Return selected table report

- [`taxaList()`](https://rtassel.maizegenetics.net/reference/taxaList.md)
  : Get list of taxa from TASSEL data

- [`taxaSummary()`](https://rtassel.maizegenetics.net/reference/taxaSummary.md)
  : Get taxa summary of genotype table

- [`traitNames()`](https://rtassel.maizegenetics.net/reference/traitNames.md)
  : Return trait names

- [`treeJavaApp()`](https://rtassel.maizegenetics.net/reference/treeJavaApp.md)
  : R interface for Archaeopteryx interactive tree viewer

- [`unionJoin()`](https://rtassel.maizegenetics.net/reference/unionJoin.md)
  : Union join phenotype tables

# Articles

### Articles

- [Installing
  rTASSEL](https://rtassel.maizegenetics.net/articles/rtassel_installation.md):
- [Filtering Genotype
  Tables](https://rtassel.maizegenetics.net/articles/genotype_filtration.md):
- [rTASSEL
  Benchmarks](https://rtassel.maizegenetics.net/articles/rtassel_benchmarks.md):