Skip to contents

Prepare Input Files for PowerCore

Source: R/prep_powercore_input.R
prep_powercore_input.Rd

Prepare input files for PowerCore, a program applying the advanced M strategy with a heuristic search for establishing core sets (Kim et al. 2007; Kim et al. 2007) .

Usage

prep_powercore_input(
  data,
  genotype,
  qualitative,
  quantitative,
  center = TRUE,
  scale = TRUE,
  always.selected = NULL,
  file.name = "PowerCore_input",
  folder.path = getwd()
)

Arguments

data

The data as a data frame object. The data frame should possess columns with the genotype names and multiple quantitative and/or qualitative trait/variable data.

genotype

Name of column with the genotype names as a character string.

qualitative

Name of columns with the qualitative traits as a character vector.

quantitative

Name of columns with the quantitative traits as a character vector.

center

either a logical value or numeric-alike vector of length equal to the number of columns of x, where ‘numeric-alike’ means that as.numeric(.) will be applied successfully if is.numeric(.) is not true.

scale

either a logical value or a numeric-alike vector of length equal to the number of columns of x.

always.selected

A character vector with names of individuals in the genotype that should always be selected in the core collection. The maximum length accepted by MStrat is 500.

file.name

A character string of name of file where the data will be saved.

folder.path

The path to folder where the input files are to be saved.

References

Kim K, Chung H, Cho G, Ma K, Chandrabalan D, Gwag J, Kim T, Cho E, Park Y (2007). “PowerCore: A program applying the advanced M strategy with a heuristic search for establishing core sets.” Bioinformatics, 23(16), 2155–2162.

Kim K, Chung H, Cho G, Ma K, Chandrabalan D, Gwag J, Kim T, Cho E, Park Y (2007). “PowerCore (v. 1.0): A Program Applying the Advanced M Strategy Using Heuristic Search for Establishing Core or Allele Mining Sets - User Manual.” Genetic Resources Division, National Institute of Agricultural Biotechnology (NIAB), Rural Development Administration (RDA), R. Korea.

Examples


library(EvaluateCore)

data(cassava_EC)
data <- cassava_EC

quant <- c("NMSR", "TTRN", "TFWSR", "TTSW", "TTPW", "AVPW",
           "ARSR", "SRDM")
qual <- c("CUAL", "LNGS", "LFRT", "LBTEF", "CBTR", "NMLB",
          "ANGB", "CUAL9M", "LVC9M", "TNPR9M", "PL9M", "STRP", "STRC",
          "PSTR")

# Prepare genotype column
data$Accession <- rownames(data)
rownames(data) <- NULL
data$Accession <- as.factor(data$Accession)

# Convert qualitative data as factors
data[, qual] <- lapply(data[, qual],
                       function(x) factor(as.factor(x)))

sel <- c("TMe-2906", "TMe-3412", "TMe-1374", "TMe-768", "TMe-14",
         "TMe-3284", "TMe-937", "TMe-1859", "TMe-3265", "TMe-1739",
         "TMe-972", "TMe-769", "TMe-3243", "TMe-3719", "TMe-1095",
         "TMe-893", "TMe-1262", "TMe-2083", "TMe-376", "TMe-3633",
         "TMe-1738", "TMe-2428", "TMe-259", "TMe-3457", "TMe-1406",
         "TMe-977", "TMe-3006", "TMe-925", "TMe-3671", "TMe-2779",
         "TMe-1293", "TMe-268", "TMe-266", "TMe-3562", "TMe-801")

prep_powercore_input(data = data, genotype = "Accession",
                     qualitative = qual, quantitative = quant,
                     center = TRUE, scale = TRUE,
                     always.selected = sel,
                     file.name = "PowerCore_input",
                     folder.path = tempdir())
#> PowerCore output file created at /var/folders/2s/h6hvv9ps03xgz_krkkstvq_r0000gn/T//RtmpnQmFgO/PowerCore_input.csv