- 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.
- 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
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.
-
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 argumentsnpsubset
which allows only a subset of the SNPs in the RA file to be read in. -
makeUR
function now has argumentindsubset
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.
This is the first release of GUSbase. This package forms a base for reading in data into the GUSverse.
- Converting VCF files into reference/alternate (RA) count format.
- Reading RA format into R.
- Creating Unrelated populations
- Transformation functions used in the GUSverse
- Additionally features are due to be added on to this package as the other packages of the GUSverse are developed and released to CRAN.
- 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).