blup: blup

Description Usage Arguments Value Author(s) Examples

View source: R/blup.R

Description

Performs the Best Linear Unbiased Prediction (BLUP)

Usage

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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 <pengzhao@nwafu.edu.cn>

Examples

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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.