readGenotypePhenotype: Wrapper function of TasselGenotypePhenotype class for...

In maize-genetics/bioconductor_test: R front-end for TASSEL

Description

Creates a Java GenotypePhenotype object which is used for TasselGenotypePhenotype object construction. The Java GenotypePhenotype object is created via an intersect method from TASSEL.

Usage

readGenotypePhenotype(genoPathOrObj, phenoPathDFOrObj, ...)

Arguments

genoPathOrObj	a path to a genotype file (e.g. VCF, hmp, etc.) or TASSEL Genotype Obj
phenoPathDFOrObj	a path, a data frame of phenotypic data, or TASSEL Phenotype Obj
...	Additional parameters to be sent to the function. Currently, if an R data frame object is passed, additional parameters will also need to be entered for this process. These parameters are derived from the readPhenotypeFromDataFrame function. Mainly, taxaID is required. If you would like to specify depth retention and position sorting in Genotype Tables from a path, indicate them here. See readGenotypeTableFromPath() for more detail.

Value

Returns an object of TasselGenotypePhenotype class.

maize-genetics/bioconductor_test documentation built on Nov. 4, 2019, 5:19 p.m.