blup: blup

In Phenotype: A Tool for Phenotypic Data Processing

Description

Performs the Best Linear Unbiased Prediction (BLUP)

Usage

blup(
  x,
  sample = NULL,
  year = NULL,
  loc = NULL,
  rep = NULL,
  phe = NULL,
  fold = 1.5
)

Arguments

x	Input phenotype data file.
sample	The column name of the sample name in phenotypic data. (Default: NULL)
year	The column name of the year in phenotypic data. (Default: NULL)
loc	The column name of the location in phenotypic data. (Default: NULL)
rep	The column name of the replication in phenotypic data. (Default: NULL)
phe	The column name of the phenotypic value in data. (Default: NULL)
fold	Fold before inter-quartile range. (Default: 1.5)

Value

Estimate BLUPs for a phenotypic data with outliers removed on a per sample basis.

Author(s)

Peng Zhao <[e-mail]>

Examples

data("wheatds")
blup_out <- blup(wheatds, sample = "Line", loc = "Env", rep = "Rep", phe = "DS")

Example output

Heritability = 0.844049387374586 
Warning messages:
1: grouping factors must have > 1 sampled level 
2: grouping factors with < 5 sampled levels may give unreliable estimates 
3: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  unable to evaluate scaled gradient
4: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge: degenerate  Hessian with 1 negative eigenvalues

Phenotype documentation built on Aug. 6, 2020, 5:10 p.m.