R/write_stockr.R
write_stockr.RdWrite a stockR dataset (Fost et al. submitted). Used internally in radiator and might be of interest for users.
write_stockr(data, filename = NULL, verbose = TRUE)(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.
(optional) The stockr object is written in the working
directory. The file is written with radiator_stockr_DATE@TIME.RData and
can be open with readRDS.
Default: filename = NULL.
(optional, logical) When verbose = TRUE
the function is a little more chatty during execution.
Default: verbose = TRUE.
The object generated is a matrix with
dimension: MARKERS x INDIVIDUALS. The genotypes are coded like PLINK:
0, 1 or 2 alternate allele. 0: homozygote for the reference allele,
1: heterozygote, 2: homozygote for the alternate allele.
Missing genotypes have NA. The object also as 2 attributes.
attributes(data)$grps with STRATA/POP_ID of the individuals and
attributes(data)$sample.grps filled with INDIVIDUALS.
Both attributes can be used inside stockR.
Foster et al. submitted