Write a stockR dataset from a tidy data frame or GDS file or object.
Source:R/write_stockr.R
write_stockr.RdWrite a stockR dataset (Fost et al. submitted). Used internally in genometranslator and might be of interest for users.
Arguments
- data
A supported genomic file, object, or tidy genomic data frame. Default:
data = NULL.- filename
(optional) The stockr object is written in the working directory. The file is written with
radiator_stockr_DATE@TIME.RDataand can be open with readRDS. Default:filename = NULL.- verbose
Logical indicating whether progress messages are emitted. Default:
verbose = TRUE.
Value
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.
Data filtering
This writer does not silently filter markers or individuals. It may validate requirements imposed by the destination format and stop with an informative error when the input is unsuitable. It is the user's responsibility to filter and quality-control the data appropriately for the intended analysis before generating the output. Use radr or another suitable workflow when filtering is required.
Dependencies
Required package dependencies are declared in DESCRIPTION and are
installed with genometranslator. Any additional dependency needed only
for this format or option is identified in this help page. Use
genometranslator_dependencies() to inspect the availability of core
packages, optional packages, and external executables.
Author
Thierry Gosselin thierrygosselin@icloud.com