write_ldna: Write a LDna object from a tidy data frame

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

Write a LDna object from a tidy data frame

Description

Write a LDna object from a biallelic tidy data frame. Used internally in radiator and might be of interest for users.

Usage

write_ldna(
  data,
  filename = NULL,
  parallel.core = parallel::detectCores() - 1,
  ...
)

Arguments

data	A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? Look into radiator tidy_genomic_data. The genotypes are biallelic.
filename	(optional) The file name of the LDna lower matrix file. Radiator will append .ldna.rds to the filename. If filename chosen is already present in the working directory, the default radiator_datetime.ldna.rds is chosen. With default, filename = NULL, no file is generated, only an object in the Global Environment. To read the data back into R, use readRDS("filename.ldna.rds").
parallel.core	(optional) The number of core used for parallel execution during import. Default: parallel.core = parallel::detectCores() - 1.
...	(optional) To pass further argument for fine-tuning the function (see details).

Details

The function requires SNPRelate to prepare the data for LDna.

To install SNPRelate: install.packages("BiocManager") BiocManager::install("SNPRelate")

To install LDna: devtools::install_github("petrikemppainen/LDna")

Author(s)

Thierry Gosselin [e-mail]

References

Kemppainen P, Knight CG, Sarma DK et al. (2015) Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure. Molecular Ecology Resources, 15, 1031-1045.

Zheng X, Levine D, Shen J, Gogarten SM, Laurie C, Weir BS. (2012) A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics. 28: 3326-3328. doi:10.1093/bioinformatics/bts606

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