Man pages for maize-genetics/rTASSEL
R Front-End for TASSEL
| as.matrix.TasselDistanceMatrix | Coerce matrix from TasselDistanceMatrix class |
| as.matrix.TasselGenotypePhenotype | Coerce genotype table to R matrix |
| AssociationResultsBLUE-class | AssociationResultsBLUE Class |
| AssociationResults-class | AssociationResults Class |
| AssociationResultsFast-class | AssociationResultsFast Class |
| AssociationResultsGLM-class | AssociationResultsGLM Class |
| AssociationResultsMLM-class | AssociationResultsMLM Class |
| AssociationResults-validity | AssociationResults validation |
| associationType | Return GWAS association type |
| assocModelFitter | R interface for TASSEL's association methods |
| asTasselDistanceMatrix | Coerce matrix to TasselDistanceMatrix object |
| colnames-TasselDistanceMatrix-method | Column names |
| concatenate | Concatenate phenotype tables |
| createTree | R interface for TASSEL's tree creation methods |
| dim-TasselDistanceMatrix-method | Get dimensions of TasselDistanceMatrix object |
| distanceMatrix | Create a TASSEL distance matrix |
| exportGenotypeTable | Export Genotype Table to Disk |
| filterGenotypeTableBySiteName | Filter genotype table by site IDs |
| filterGenotypeTableSites | Filter genotype table by sites |
| filterGenotypeTableTaxa | Filter genotype table by taxa |
| genomicPrediction | R interface for TASSEL's genomic prediction capabilities |
| getPhenotypeDF | Get an R/'DataFrame' phenotype data frame from TASSEL object |
| getSumExpFromGenotypeTable | Create Summarized Experiment from a TASSEL Genotype Table |
| imputeLDKNNi | LD KNNi imputation |
| imputeNumeric | Imputation methods in Numerical Transformations |
| intersectJoin | Intersect join phenotype tables |
| kinshipMatrix | Create a TASSEL kinship matrix |
| ldJavaApp | Linkage desequilibrium visualization application |
| ldPlot | Linkage disequilibrium plot |
| linkageDiseq | Calculate linkage disequilibrium from an rTASSEL genotype... |
| mds | Run MDS on 'TasselDistanceMatrix' objects |
| mergeGenotypeTables | Merge genotype tables |
| ncol-TasselDistanceMatrix-method | Number of columns |
| nrow-TasselDistanceMatrix-method | Number of rows |
| pca | Run PCA on Genotype Table |
| PCAResults-class | PCAResults Class |
| PCAResults-validity | PCAResults validation |
| plotManhattan | Create a Manhattan plot from rTASSEL association output |
| plotManhattanQC | Create a QC Manhattan plots from rTASSEL association output |
| plotPCA | Generate PCA plot |
| plotQQ | Create a QQ plot from rTASSEL association output |
| plotScree | Generate scree plots |
| positionList | Get position list metadata from genotype table |
| readGenotypePhenotype | Wrapper function of TasselGenotypePhenotype class for... |
| readGenotypeTableFromGigwa | Read genotype data from GIGWA using QBMS |
| readGenotypeTableFromPath | Wrapper function of TasselGenotypePhenotype class for... |
| readPhenotypeFromDataFrame | Wrapper function of TasselGenotypePhenotype class for... |
| readPhenotypeFromPath | Wrapper function of TasselGenotypePhenotype class for... |
| readTasselDistanceMatrix | read TASSEL distance matrix object from file |
| reportNames | Return report names |
| rownames-TasselDistanceMatrix-method | Row names |
| rtPaths | Paths to TASSEL toy data |
| seqDiversity | Calculate sequence diversity |
| siteSummary | Get site summary of genotype table |
| startLogger | Start TASSEL logging information |
| tableReport | Return selected table report |
| TasselDistanceMatrix-class | TasselDistanceMatrix Class |
| TasselGenotypePhenotype-class | TasselGenotypePhenotype Class |
| taxaList | Get list of taxa from TASSEL data |
| taxaSummary | Get taxa summary of genotype table |
| traitNames | Return trait names |
| treeJavaApp | R interface for Archaeopteryx interactive tree viewer |
| unionJoin | Union join phenotype tables |
