Description Usage Arguments Value Details Examples
Combines Peaky's fine-mapping results, generated separately for each bait, into a single table and stores it on disk. Marginal posterior probabilities of contact (MPPC) are in its 'rjmcmc_pos' column. Other columns' values are described in the vignette. Generates a .pdf plot for each bait by default.
1 | peaky_wrapup(peaky_output_dir, plots = TRUE, ...)
|
peaky_output_dir |
Directory which Peaky's intermediate files and results are stored in. Needs a baits_rjmcmc folder generated by |
plots |
Whether or not to generate a .pdf plot for each bait with |
... |
further arguments to be passed to |
List containing the output directory where the table is stored, and the table itself.
This function checks for bait_rjmcmc_*.rds files in peaky_output_dir/baits_rjmcmc, reads them, collates them, and optionally plots them.
1 2 3 4 5 6 7 8 9 10 11 12 13 | base = system.file("extdata",package="peaky")
chicago_rds_path = paste0(base,"/chicago_output.rds")
peaky_output_dir = paste0(base,"/peaky_from_chicago")
## Not run:
peaky_prepare_from_chicago(chicago_rds_path, peaky_output_dir, subsample_size=NA)
#Big dataset? Consider subsample_size=10e3 for speed.
for(i in 1:3){ peaky_run(peaky_output_dir,i) }
#Tip: run this in parallel on a cluster by scheduling an array job and passing its elements to i.
peaky_wrapup(peaky_output_dir)
## End(Not run)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.