NEWS.md
In corto: Inference of Gene Regulatory Networks

corto 1.3.1

New filter_regulon() and getregulon() helpers for post-processing a regulon: subset it by centroid, likelihood and absolute correlation, and flatten it into a data frame of edges with optional tab-separated export. Proposed by Hugo Tovar (#15).
mra() now performs Signature Master Regulator Analysis when expmat1 is provided as a named vector, as the documentation had always described. The null model permutes the signature values across feature names, and nperm defaults to 1000 in this mode. Thanks to Hugo Tovar for the detailed diagnosis and a reference implementation (#13).

Sample-by-sample mra() (a single expmat1, no expmat2) now returns the same list as the other modes, list(nes, pvalue, sig, regulon), instead of a bare matrix. Use mra(expmat, regulon=regulon)$nes to get the previous output (#1).

corto() failed with invalid 'row.names' length when a single centroid was provided. The internal correlation step dropped to a vector and lost its row names. Thanks to Hualin Wang for the fix (#6, #14).
Sample-by-sample mra() returned an all-NA matrix whenever any regulon target had zero variance in the input matrix. The permuted null signatures were not NA-guarded the way the real signature was.
gsea() errored on R >= 4.2 when method was left at its default, since the default is a length-2 vector. It now uses match.arg() and defaults to "permutation" as before.
plot_gsea(omit_middle=TRUE) errored on an undefined legend_position.
mraplot() errored on regulons with fewer than 12 targets, which is reachable with the default minsize=10.
ssgsea(scale=TRUE) silently dropped the sample names from the returned NES matrix.
mra() failed on regulons left with a single centroid after minsize filtering.
mraplot() now stops with an informative message when given sample-by-sample results, which it cannot plot.
The CNV correction step dropped to a vector when cnvmat and inmat had a single sample or a single target in common, the same dimension-drop problem fixed elsewhere. Guarded with drop=FALSE.
corto() now stops with an informative message when no edge passes the correlation threshold, instead of failing on an invalid row name.

corto() is roughly 1.2x faster single-threaded and 1.4x faster on 4 threads. The input matrix is transposed once instead of once per bootstrap and is no longer shipped twice to the workers, DPI selection is done by a radix sort rather than a grouped data frame, and the regulon is assembled in one pass instead of rescanning the edge table for every centroid. Results are bit-identical to previous versions.

dplyr and gplots are no longer required, which removes about 20 recursive dependencies and makes installation considerably faster. knitr and rmarkdown moved from Imports to Suggests, grDevices and graphics added.
Documented defaults corrected for scatter(bgcol=), val2col(nbreaks=) and plot_gsea2().