
#### Available Example Datasets

VIEWpoly provides example datasets to help you get started:

- **Potato - Atlantic x B1829-5**: A tetraploid example containing complete linkage map and QTL analysis for a subset of individuals

Access complete example datasets at [polyploids.org](https://www.polyploids.org/input-tests)

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#### Upload Linkage Map Files

##### MAPpoly Output

Upload linkage maps built with the [MAPpoly](https://cran.r-project.org/web/packages/mappoly/index.html) package:

- **Required file**: Object of class `mappoly.map` (RData format)
- **Tutorial**: [MAPpoly vignette](https://rpubs.com/mmollin/tetra_mappoly_vignette)
- **VIEWpoly integration**: [How to prepare MAPpoly outputs](https://cristianetaniguti.github.io/viewpoly_vignettes/VIEWpoly_tutorial.html#Upload_linkage_map_files)

##### polymapR Output

Upload linkage maps built with the [polymapR](https://cran.r-project.org/web/packages/polymapR/index.html) package:

- **Required files**: 
  - `polymapR.dataset.RData`
  - `polymapR.map.RData`
- **Data type**: Select discrete or probabilistic genotype input
- **Ploidy**: Specify ploidy level (4 or 6)
- **Tutorial**: [polymapR vignette](https://cran.r-project.org/web/packages/polymapR/vignettes/Vignette_polymapR.html)

##### OneMap Output

Upload linkage maps for diploid populations built with [OneMap](https://cristianetaniguti.github.io/Tutorials/onemap/):

- **Required file**: Object of class `viewmap` (RData format)
- **Supported populations**: Outcrossing and inbred-based populations

##### Custom Format

Upload linkage map files in standard format (CSV, TSV, or TSV.GZ):

- **dosages.tsv**: Marker dosage data
- **genetic_map.tsv**: Genetic map positions
- **phases.tsv**: Parental phase information
- **marker information** (optional): Marker ID, genome position, chromosome

Download example files using the provided radio buttons.

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#### Upload QTL Analysis Files

##### QTLpoly Output

Upload QTL analysis results from [QTLpoly](https://github.com/gabrielgesteira/QTLpoly):

- **Required files**:
  - `QTLpoly_data.RData` (class: qtlpoly.data)
  - `QTLpoly_remim.mod.RData` (class: qtlpoly.remim)
  - `QTLpoly_est.effects.RData` (class: qtlpoly.effects)
  - `QTLpoly_fitted.mod.RData` (class: qtlpoly.fitted)
- **Tutorial**: [QTLpoly tutorial](https://gabrielgesteira.github.io/QTLpoly/docs/1-tutorial)

##### diaQTL Output

Upload QTL analysis from [diaQTL](https://github.com/jendelman/diaQTL):

- **Required files**:
  - `diaQTL_scan1_list.RData`
  - `diaQTL_scan1.summaries_list.RData`
  - `diaQTL_BayesCI_list.RData`
  - `diaQTL_fitQTL_list.RData`
- **Tutorial**: [diaQTL vignette](https://jendelman.github.io/diaQTL/diaQTL_Vignette.html)

##### polyqtlR Output

Upload QTL analysis from [polyqtlR](https://cran.r-project.org/web/packages/polyqtlR/index.html):

- **Required files**:
  - `polyqtlR_effects.RData`
  - `polyqtlR_qtl_info.RData`
  - `polyqtlR_QTLscan_list.RData`
- **Tutorial**: [polyqtlR vignette](https://cran.r-project.org/web/packages/polyqtlR/vignettes/polyqtlR_vignette.html)

#### Custom QTL Format

Upload QTL results in standard format (CSV, TSV, or TSV.GZ):

- **selected_mks.tsv**: Selected markers
- **qtl_info.tsv**: QTL information
- **blups.tsv**: Best Linear Unbiased Predictions
- **beta.hat.tsv**: Estimated effects
- **profile.tsv**: QTL profile
- **effects.tsv**: Allelic effects
- **probs.tsv**: Genotype probabilities

Download example files using the provided radio buttons.

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#### Upload Genome Browser Files

Upload genomic data for candidate gene exploration using [JBrowseR](https://gmod.github.io/JBrowseR/):

**⚠️ Warning**: All genome files must be from the same genome version used to build the genetic map.

##### Genome Assembly (Required to access features of 'Genome' tab)

- **Local files**: Upload `.fasta/.fasta.gz` with index files (`.fai`, `.gzi`)
- **Hosted URL**: Provide URL to hosted FASTA file (faster loading)

##### Annotation (Optional)

- **Local files**: Upload `.gff3/.gff3.gz` with `.gff3.tbi/.gff3.gz.tbi` index
- **Hosted URL**: Provide URL to hosted GFF3 file

##### Variants (Optional)

- **Local files**: Upload `.vcf` with `.vcf.tbi` index
- **Hosted URL**: Provide URL to hosted VCF file

##### Alignments (Optional)

- **Local files**: Upload `.bam` with `.bam.bai` or `.cram` with `.cram.crai`
- **Hosted URL**: Provide URL to hosted BAM/CRAM file

##### BigWig Data (Optional)

- **Local files**: Upload `.wig` file
- **Hosted URL**: Provide URL to hosted WIG file

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#### Upload HIDECAN Files

Upload GWAS, differential expression, and candidate gene data for [HIDECAN](https://cran.r-project.org/web/packages/hidecan/index.html) visualization:

##### GWAS Output

- [**GWASpoly**](https://github.com/jendelman/GWASpoly): Object of class `GWASpoly.thresh` (from `GWASpoly::set.threshold()`)
- **Custom GWAS**: CSV file with GWAS results

##### Differential Expression & Candidate Genes

- **DE.csv**: Differential expression results
- **CAN.csv**: Candidate genes information

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#### VIEWpoly Dataset Management

##### Download VIEWpoly Dataset

Save your uploaded data in VIEWpoly format:

- Converts map and QTL data to VIEWpoly format
- **Note**: Genome information is not stored
- Define a dataset name (no spaces)

##### Upload VIEWpoly Dataset

Load previously saved VIEWpoly datasets:

- Upload `.RData` files containing VIEWpoly objects
- The app automatically detects VIEWpoly objects in your R environment

### Additional Resources

**VIEWpoly Tutorial**: [https://cristianetaniguti.github.io/viewpoly_vignettes/](https://cristianetaniguti.github.io/viewpoly_vignettes/)

**MAPpoly Tutorial**: [https://rpubs.com/mmollin/tetra_mappoly_vignette](https://rpubs.com/mmollin/tetra_mappoly_vignette)

**QTLpoly Tutorial**: [https://gabrielgesteira.github.io/QTLpoly/docs/1-tutorial](https://gabrielgesteira.github.io/QTLpoly/docs/1-tutorial)

**polyQTLR Tutorial**: [https://cran.r-project.org/web/packages/polyqtlR/vignettes/polyqtlR_vignette.html](https://cran.r-project.org/web/packages/polyqtlR/vignettes/polyqtlR_vignette.html)

**polymapR Tutorial**: [https://cran.r-project.org/web/packages/polymapR/vignettes/Vignette_polymapR.html](https://cran.r-project.org/web/packages/polymapR/vignettes/Vignette_polymapR.html)

**diaQTL Tutorial**: [https://jendelman.github.io/diaQTL/diaQTL_Vignette.html](https://jendelman.github.io/diaQTL/diaQTL_Vignette.html)

**OneMap Tutorial**: [https://cristianetaniguti.github.io/Tutorials/onemap/](https://cristianetaniguti.github.io/Tutorials/onemap/)

**JBrowse Documentation**: [https://jbrowse.org/jb2/](https://jbrowse.org/jb2/)

**HIDECAN Documentation**: [https://plantandfoodresearch.github.io/hidecan/](https://plantandfoodresearch.github.io/hidecan/)

**GWASpoly Tutorial**: [https://potatobreeding.cals.wisc.edu/software/](https://potatobreeding.cals.wisc.edu/software/)

**Tools for Polyploids**: [https://www.polyploids.org/](https://www.polyploids.org/)

**Breeding Insight**: [https://www.breedinginsight.org](https://www.breedinginsight.org)
