update.cross: update.cross
In nnavarro/shapeQTL: shape QTL mapping experiment using R

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/utils_shape.R

Update phenotypes and covariates in a cross qtl object. New phenotypes (for ex. tangent coordinates) are merged to an existing cross object obtained from read.cross

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## S3 method for class 'cross'
update(cross, new.pheno = NULL, phen2keep = NULL,
  phen2update = NULL, id.geno = NULL, na.rm = FALSE, ...)

`cross`	A cross object containing genotypes and some phenotypes
`new.pheno`	An optional data.frame containing new phenotypes
`phen2keep`	An optional vector with names of the original phenotypes to keep
`phen2update`	An optional vector with names of the subset of new phenotypes to keep
`id.geno`	An optional vector with the matching id in the genotypes
`na.rm`	An optional logical if individuals with missing phenotypes should be removed from the cross

Function takes a cross object and a dataframe with new phenotypes (tangent coordinates, PC scores,...), matches cross$pheno$ID to the id column of the new phenotypes. Matching id.geno may be provide as an optional input parameter. Additional covariates may be provided as supplementary arguments but their ordering must match to the new phenotypes.

Function returns the cross object with updated phenotypes.

Nicolas Navarro

read.cross

data(fake.bc)
tgCoords <- data.frame(1:nind(fake.bc), rnorm(nind(fake.bc)), rnorm(nind(fake.bc)))
colnames(tgCoords) <- c('Id', 'ProcCoord1','ProcCoord2')
fake.bc <- update.cross(fake.bc, new.pheno=tgCoords, phen2keep=c("sex","age"), phen2update=colnames(tgCoords)[grep("ProcCoord",colnames(tgCoords))])