https://github.com/breeding-insight/bigr - v0.5.5

This PR focuses on function updates, documentation improvements, and bug fixes in preparation for the CRAN submission. Key changes include improved messaging in functions (using message() in place of cat()), enhanced error handling (especially in functions recovering reference/alternative alleles), and updates to documentation and examples.

• Updated function documentation and examples across several R scripts.
• Replaced cat() calls with message() for consistency in user feedback.
• Refactored error handling in functions such as addrefalt and check_ped.
• Updated the madc2vcf() function to madc2vcftargets, and changed getOffTargets() to madc2vcf_all()

- R
Published by alex-sandercock about 1 year ago

https://github.com/breeding-insight/bigr - v0.4.2

• Minor update to the check_ped() function

- R
Published by alex-sandercock over 1 year ago

https://github.com/breeding-insight/bigr - v0.4.1

Minor bug fixes

- R
Published by alex-sandercock over 1 year ago

https://github.com/breeding-insight/bigr - v0.4.0

New functions and bug fixes: - get_offTargets: obtain the target and off-target SNPs from a fixedAllele MADC file - madc2vcf: obtain the read count information for target SNPs only from a fixedAllele MADC file and convert to VCF format

- R
Published by alex-sandercock over 1 year ago

https://github.com/breeding-insight/bigr - v0.3.4

• Bug fixes

- R
Published by alex-sandercock over 1 year ago

https://github.com/breeding-insight/bigr - Bug fix v0.3.1

Fixed a bug with the filterVCF function where values in the INFO column were causing errors.

- R
Published by alex-sandercock about 2 years ago

https://github.com/breeding-insight/bigr - v0.3.0

• Updated documentation
• Updated citation information
• Added filter.VCF function to filter VCF files or vcfR objects

- R
Published by alex-sandercock about 2 years ago

https://github.com/breeding-insight/bigr - v0.2.0

Two functions have been added for this release:

• The cleanpedigree function was changed to the checkped function.
  • The function now alerts the user to the errors present within the pedigree and provides the sample IDs in conflict.
• The dosage2vcf function was added
  • This function produces a VCF file from the DArT Dose Report and DArT Counts file.

- R
Published by alex-sandercock about 2 years ago

https://github.com/breeding-insight/bigr - Initial release

Initial versioned release of the Breeding Insight Genomics R package.

- R
Published by alex-sandercock about 2 years ago