NEWS.md

In tpbilton/GUSbase: Genotyping Uncertainty with Sequencing Data: Base Package

GUSbase 0.2.3

• Add function makeRA to add user to create a RA object from count matrices of reference and alternate alleles.
• Added another data file for an example of the makeRA object.

GUSbase 0.2.1

• Comet plot can now be produced for each individual. A few bugs in the comet plot function have also been fixed
• Add a function to the RA object $mergeSamples which can merge samples in the RA object.
• Summary information in a RA object is computed once and stored to same time in recomputing

Various other bugs have been fixed

GUSbase 0.2.0

Version released for Thesis by Bilton (2020).

New plot functions added: Comet plot which is produced using $cometPlot in an RA object rocket plot which is produced using $rocketPlot in an RA object * RDD (read ratio density) plot which is produced using $RDDPlot in an RA object

Various other bugs have also been fixed.

GUSbase 0.1.1

• Added $writeVCF function to RA object. Converts the allele count data in the RA object back to a VCF file.
• Added $writeRA function to RA object. Converts the allele count data in the RA object back to an RA file.
• readRA function now has argument snpsubset which allows only a subset of the SNPs in the RA file to be read in.
• makeUR function now has argument indsubset which allows only a subset of the individuals to be retained in the creation of the UR population.

• The $p_est function in the makeUR was fixed up and is now working properly. In addition, the estimation of allele frequencies and sequencing errors have been implemented using the EM algorithm which is much faster and considerably more reliable.

• A few bugs were also fixed.

GUSbase 0.1.0

This is the first release of GUSbase. This package forms a base for reading in data into the GUSverse.

Main Functions:

• Converting VCF files into reference/alternate (RA) count format.
• Reading RA format into R.
• Creating Unrelated populations
• Transformation functions used in the GUSverse

Comments:

• Additionally features are due to be added on to this package as the other packages of the GUSverse are developed and released to CRAN.

References

• Bilton, T.P. (2020). "Developing statistical methods for genetic analysis of genotypes from genotyping-by-sequencing data" (Doctoral Thesis, University of Otago, Dunedin, New Zealand).

tpbilton/GUSbase documentation built on March 8, 2024, 1:35 p.m.