ReadZmat: Read Z matrix

Description

Read in the Z matrix that assigns groups/strains/lines to their trait measurements.

Usage

ReadZmat(filename = NULL)

Arguments

filename

contains the name of the Z matrix file. The file name needs to be in quotes. If the file is not in the working directory, then the full path to the file is required.

Value

a data matrix is returned of the Z matrix.

Details

The underlying linear mixed model is of the form $$Y = X \beta + Z u_g + e$$ where Z is a (n x $n_g$) matrix that contains ones and zeros, n is the number of trait measurements, and $n_g$ is the number of groups/strains/lines. If n and $n_g$ are the same, then there is no need to specify Z. However, if a group/strain/line has multiple trait measurements (i.e. $n > n_g$) then the Z matrix is needed to tell Eagle which trait measurements belong to which groups/strains/lines.

A space separated text file is assumed. Each row of the matrix contains multiple zeroes but only a single one. The file cannot contain column or row headings. The file also cannot contain a row of only zeroes. Here, n must be larger than $n_g$ otherwise an error will be issued.

Examples

Run this code

# NOT RUN {
# Read in  example Z matrix from ./extdata/

# find the full location of the Z matrix data 
complete.name <- system.file('extdata', 'Z.txt', package='Eagle')
  
# read in Z matrix data 
Z_obj <- ReadZmat(filename=complete.name) 
                               
# look at first few rows of the Z matrix file
head(Z_obj)


# }