NEWS.md

In TheJacksonLaboratory/CAPE: Combined Analysis of Pleiotropy and Epistasis for Diversity Outbred Mice

New in version 3.1.1

New in version 3.1.2

Bug Fixes

• Edited vignette to better explain how to set up the code and directories so that the demo code runs.

• We removed examples from function documentation that do not work outside of run_cape

New Features

• pracma::pinv() replaced pseudoinverse().

• Added param_file argument to load_input_and_run_cape().

• Added ability for cape2mpp() to recognize and format multi-parent crosses

• Added ability to read in multi-parent crosses in qtl format.

Bug Fixes

• Fixed display of marker effects in plot_singlescan().

• Updated missing parameters from load_input_and_run_cape() documentation

• Changed binary file extensions of saved files to .RData.

• Additional minor bug fixes.

New in version 3.1.0

New Features

• run_cape() now runs a full cape analysis from a yml parameter file.

• Dots were replaced with underscores in all function names.

• All code was refactored to S6.

• qtl2cape() now accepts a covariate matrix as an argument.

• Added demos starting from different file formats.

• Added formatting capabilities for PLINK files.

Bug Fixes

• bin_curve() was updated to handle very short vectors.

• Additional minor bug fixes.

• Fixed covariate handling in pairscan().

TheJacksonLaboratory/CAPE documentation built on Feb. 12, 2024, 4:32 p.m.