Mega2gdsfmt: transcode mega2 to gdsfmt/SNP_ARRAY

In Mega2R: Accessing and Processing a 'Mega2' Genetic Database

transcode mega2 to gdsfmt/SNP_ARRAY

Description

Reads the data frames in "envir" and builds a GDSFMT COREARRAY file from them.

Usage

Mega2gdsfmt(
  filename = "test.gds",
  markers = NULL,
  snp.order = FALSE,
  SeqArray = FALSE,
  envir = ENV
)

Arguments

filename	gdsfmt file to create
markers	data frame of markers to be processed
snp.order	TRUE indicates that the "genotype" data matrix has SNP as the first index which changes more quickly than subsequent indices. FALSE indicates that SAMPLE is the the first index.
SeqArray	TRUE uses SeqArray labels for the gdsfmt vector elements. FALSE it uses labels shown in SNPRelate
envir	'environment' containing SQLite database and other globals

Value

writes the "filename" file containing the CoreArray data. Then returns an internal pointer, class .gds, to the file data.

See Also

gdsfmt

Examples

db = system.file("exdata", "seqsimm.db", package="Mega2R")
ENV = read.Mega2DB(db)
gdsfmtfile = file.path(where_mega2rtutorial_data(), "test.gds")
append_genotype_a = TRUE
append_genotype_b = append_genotype_c = FALSE
gn = Mega2gdsfmt(gdsfmtfile, envir=ENV)
gn

Mega2R documentation built on May 29, 2024, 1:14 a.m.