Reading and combining SGP outputs {SFSI}

Read and combine SGP outputs

Description

Read the output generated by the 'SGP' or 'SGP.CV' functions saved at the provided save.at parameter. It merges all partial files when data was splited according to argument subset. Function 'read_summary' reads the output generated after calling the method summary; multiple outputs are read if argument path is a vector and in this case, they are combined by averaging across all outputs.

Usage

read_SGP(path = ".", type = NULL,
         file.ext = ".RData", verbose = TRUE)

read_summary(path = ".", type = NULL,
             file.ext = ".RData", verbose = TRUE)

Arguments

path

(character) Path where output files were saved. This may include a prefix

type

(character) Either 'SGP' or 'SGP.CV' to collect results generated by either function of the same name

file.ext

(character) This is the file extension at which file was saved as per the argument save.at

verbose

TRUE or FALSE to whether printing details

Value

An object of the class 'SGP' for which methods predict, plot and summary exist

Examples

  require(SFSI)
  data(wheatHTP)
  
  index = which(Y$trial %in% 1:10)    # Use only a subset of data
  Y = Y[index,]
  M = scale(M[index,])/sqrt(ncol(M))  # Subset and scale markers
  G = tcrossprod(M)                   # Genomic relationship matrix
  y = as.vector(scale(Y[,"E1"]))      # Scale response variable
  
  # Training and testing sets
  tst = which(Y$trial %in% 1:3)
  trn = seq_along(y)[-tst]
  
  path = paste0(tempdir(),"/testSGP_")
  
  # Run the analysis into 4 subsets and save them at a given path
  SGP(y, K=G, trn=trn, tst=tst, subset=c(1,4), save.at=path)
  SGP(y, K=G, trn=trn, tst=tst, subset=c(2,4), save.at=path)
  SGP(y, K=G, trn=trn, tst=tst, subset=c(3,4), save.at=path)
  SGP(y, K=G, trn=trn, tst=tst, subset=c(4,4), save.at=path)

  # Collect all results after completion
  fm = read_SGP(path)
  
  # Generate and save summary 
  summary(fm, save.at=path)
  fm2 = read_summary(path)