NEWS.md
In russHyde/coxpresdbr: Parses and Summarises Data from coxpresdb.jp

coxpresdbr (development version)

coxpresdbr 0.0.0.9000

The user can pass in a data-frame that defines the coxpresdb database; this is passed as the first argument to the function CoxpresDbAccessor(), exactly as when the file path for a CoxpresDB archive is passedto the same function. get_gene_ids and get_all_coex_partners work on the returned object, so this should be compatible with the coexpression-analysis workflows, but for datasets that fit in memory, passing a data-frame should be a lot faster. The data-frame must have columns source_id, target_id and mutual_rank.
data.table::fread is used to import data; This uses freads command line piping facility and so we use fread(cmd = "...") for security reasons. The cmd arg was introduced in data.table 1.11.6; hence the lower-bound for data.table in DESCRIPTION.
Correlation coefficients, if present in the original coxpresdb archive, are no longer reported in the coexpression partners since these coefficients are not consistently reported across the different releases of coxpresdb (and so the user can no longer filter based on these values in get_coex_partners)
User can use .tar.bz2, .tar or .zip archives as the source of CoxpresDB data and the files can be of two-column (target_id, mutual_rank) or three-column (target_id, mutual_rank, correlation_coefficient) format
Added a NEWS.md file to track changes to the package.
Added functions for importing CoxpresDB datasets from an existing archive. The functions work without having to decompress/recompress the archive. The user must have tar, grep and bzip2 installed on a unix-alike system.
Added a function for selecting subsets of the coexpression partners of a given gene (or genes): get_coex_partners. The user can select to keep the top k coexpression partners of a given gene, or any partners with a mutual rank at-most-equal to some threshold, or any partners with a correlation coefficient at-least-equal to some threshold