write_genlight: Write a genlight object from a tidy data frame or GDS file or...

In thierrygosselin/radiator: RADseq Data Exploration, Manipulation and Visualization using R

Write a genlight object from a tidy data frame or GDS file or object.

Description

Write a genlight object from a tidy data frame or GDS file or object. Used internally in radiator and might be of interest for users.

Usage

write_genlight(
  data,
  biallelic = TRUE,
  write = FALSE,
  dartr = FALSE,
  verbose = FALSE,
  parallel.core = parallel::detectCores() - 2
)

Arguments

data	(4 options) A file or object generated by radiator: tidy data Genomic Data Structure (GDS) How to get GDS and tidy data ? Look into tidy_genomic_data, read_vcf or tidy_vcf.
biallelic	(logical, optional) If you already know that the data is biallelic use this argument to speed up the function. Default: biallelic = TRUE.
write	(logical, optional) To write in the working directory the genlight object. The file is written with [e-mail] and can be open with load or readRDS. Default: write = FALSE.
dartr	(logical, optional) For non-dartR users who wants to have a genlight object ready for the package. This option transfer or generates: CALL_RATE, AVG_COUNT_REF, AVG_COUNT_SNP, REP_AVG, ONE_RATIO_REF, ONE_RATIO_SNP. These markers metadata are stored into the genlight slot: genlight.obj@other$loc.metrics. Use the radiator generated GDS data for best result. Default: dartr = FALSE.
verbose	(optional, logical) When verbose = TRUE the function is a little more chatty during execution. Default: verbose = TRUE.
parallel.core	(optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.

Author(s)

Thierry Gosselin [e-mail]

References

Jombart T (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24, 1403-1405.

Jombart T, Ahmed I (2011) adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics, 27, 3070-3071.

Examples

## Not run: 
# With defaults:
turtle <- radiator::write_genlight(data = "my.radiator.gds.rad")

# Write gl object in directory:
turtle <- radiator::write_genlight(data = "my.radiator.gds.rad", write = TRUE)

# Generate a dartR ready genlight and verbose = TRUE:
turtle <- radiator::write_genlight(
    data = "my.radiator.gds.rad",
    write = TRUE,
    dartr = TRUE,
    verbose = TRUE
 )

## End(Not run)

thierrygosselin/radiator documentation built on Nov. 7, 2024, 1:30 p.m.