NEWS.md
In fboehm/qtl2pleio: Testing Pleiotropy in Multiparental Populations
qtl2pleio 1.4.3.9000
Major changes
- None
Minor changes
- Started using Github Actions for continuous integration testing.
qtl2pleio 1.4.3
Major changes
- None
Minor changes
- Updated RcppExports.cpp and deleted C++ test files that aren't used.
qtl2pleio 1.4.2.9000
Major changes
- added function
convert_to_scan1_output to convert multivariate, one-QTL lods to output format of qtl2::scan1, for use in qtl2::bayes_int.
Minor changes
- None
qtl2pleio 1.4.1
Major changes
- None
Minor changes
- Added vignette to .Rbuildignore to ease CRAN submission.
qtl2pleio 1.4.0
Major changes
- Refactored
scan_pvl and boot_pvl to reduce duplicated code
- Added functions for genomewide, multivariate, one-QTL scan
Minor changes
- Returned to parallelization implemented by R package
parallel.
- Set default
cores value to parallelly::availableCores() for compatibility with job schedulers.
qtl2pleio 1.3.0
Major changes
- Replaced
parallel package use with furrr. This led to removal of the argument
n_cores from both boot_pvl and scan_pvl. A user may now use future::plan to
run in parallel.
- Moved vignettes to website: https://fboehm.us/software/qtl2pleio
Minor changes
- Fixed argument name in
boot_pvl, changing nboot_per_job to nboot.
- Created function
scan_pvl_clean to be called in both scan_pvl and boot_pvl. This change shouldn't affect most users' experiences.
qtl2pleio 1.2.4
Major changes
- None
Minor changes
- Updated
calc_lrt_tib function to accommodate d-dimensional, d-variate scans
qtl2pleio 1.2.3
Major changes
- None
Minor changes
-
I shortened title per CRAN recommendation
-
I added \value tags to document functions' outputs
qtl2pleio 1.2.2
Major changes
- I added data to package to enable vignettes, examples, and tests.
Minor changes
-
Per CRAN submission feedback, I spelled out QTL in DESCRIPTION file and upon first use in vignettes.
-
Added citations with references to vignettes.
qtl2pleio 1.2.1
Major changes
- none
Minor changes
- removed examples' and vignettes' dependencies on qtl2 R package.
qtl2pleio 1.2.0
Major changes
- changed output of scan_pvl to be log10 likelihood, not log (natural base) likelihood. Thank you to @HongHe0123 for suggesting this.
Minor changes
- changed column name for tibble outputs to reflect log base 10 instead of log natural base.
qtl2pleio 1.1.0
Major changes
- rewrites (and deletions) of tibble helper functions
- major revisions to code in main vignette
Minor changes
- fixed CITATION after G3 publication
qtl2pleio 1.0.7
Major changes
- None
Minor changes
- fixed Description field of DESCRIPTION file per feedback from CRAN
qtl2pleio 1.0.6
Major changes
- None
Minor changes
- removed Additional_repositories field from DESCRIPTION
qtl2pleio 1.0.5
Major changes
- None
Minor changes
- added cran-comments.md file via devtools & added it to .Rbuildignore
qtl2pleio 1.0.4
Major changes
- None
Minor changes
- Added Additional_repositories field to DESCRIPTION file per https://cran.r-project.org/submit.html in preparation for CRAN submission.
- Added url for Jiang and Zeng 1995 GENETICS article, per https://cran.r-project.org/submit.html.
qtl2pleio 1.0.3
Major changes
- Revisions per peer review at Journal of Open Source Software
Minor changes
- None
qtl2pleio 0.1.3
Major changes
- Submitted paper.md to JOSS
Minor changes
- Minor updates to recla vignette to download precalculated founder allele dosages
qtl2pleio 0.1.2.9002
Major changes
- changed default behavior of
plot_pvl to not indicate univariate peak positions.
- fixed CITATION file to tell users to cite Biorxiv preprint (following CITATION file format of rqtl/qtl2)
Minor changes
- Removed hex logo file from repo and deleted it from README
- revised paper.md in preparation for JOSS submission
Bug fixes
-
Re-created profile LOD plots for vignettes and README without indicating univariate peak positions.
-
Added line type arguments to plot_pvl.
qtl2pleio 0.1.2.9001
Major changes
- added a vignette for HTCondor & bootstrap analysis
- updated README.Rmd and README.md (per suggestions & PR of @kbroman)
qtl2pleio 0.1.2.9000
Major changes
- added inst/CITATION file
- aligned ordering and names of arguments for both
boot_pvl and scan_pvl
- added examples for
boot_pvl
- added literature references to both
boot_pvl and scan_pvl
Bug fixes
- corrected typo in vignette
qtl2pleio 0.1.2
Major changes
- added tests & examples for
scan_pvl
- changed output of
scan_pvl to a tibble
- added
boot_n function for use in bootstrap analyses
- started using covariates in calls to
calc_covs. Note that we still don't use genetic data when calling calc_covs.
- deprecated
calc_loglik_bvlmm
qtl2pleio 0.1.1
Major changes
- restructured
scan_pvl to allow for more than two phenotypes. Now output is a dataframe.
qtl2pleio 0.1.0
Major changes
- Added a
NEWS.md file to track changes to the package.
fboehm/qtl2pleio documentation built on July 17, 2021, 11:34 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
qtl2pleio 1.4.3.9000
Major changes
- None
Minor changes
- Started using Github Actions for continuous integration testing.
qtl2pleio 1.4.3
Major changes
- None
Minor changes
- Updated RcppExports.cpp and deleted C++ test files that aren't used.
qtl2pleio 1.4.2.9000
Major changes
- added function
convert_to_scan1_outputto convert multivariate, one-QTL lods to output format ofqtl2::scan1, for use inqtl2::bayes_int.
Minor changes
- None
qtl2pleio 1.4.1
Major changes
- None
Minor changes
- Added vignette to .Rbuildignore to ease CRAN submission.
qtl2pleio 1.4.0
Major changes
- Refactored
scan_pvlandboot_pvlto reduce duplicated code - Added functions for genomewide, multivariate, one-QTL scan
Minor changes
- Returned to parallelization implemented by R package
parallel. - Set default
coresvalue toparallelly::availableCores()for compatibility with job schedulers.
qtl2pleio 1.3.0
Major changes
- Replaced
parallelpackage use withfurrr. This led to removal of the argumentn_coresfrom bothboot_pvlandscan_pvl. A user may now usefuture::planto run in parallel. - Moved vignettes to website: https://fboehm.us/software/qtl2pleio
Minor changes
- Fixed argument name in
boot_pvl, changingnboot_per_jobtonboot. - Created function
scan_pvl_cleanto be called in bothscan_pvlandboot_pvl. This change shouldn't affect most users' experiences.
qtl2pleio 1.2.4
Major changes
- None
Minor changes
- Updated
calc_lrt_tibfunction to accommodate d-dimensional, d-variate scans
qtl2pleio 1.2.3
Major changes
- None
Minor changes
-
I shortened title per CRAN recommendation
-
I added \value tags to document functions' outputs
qtl2pleio 1.2.2
Major changes
- I added data to package to enable vignettes, examples, and tests.
Minor changes
-
Per CRAN submission feedback, I spelled out QTL in DESCRIPTION file and upon first use in vignettes.
-
Added citations with references to vignettes.
qtl2pleio 1.2.1
Major changes
- none
Minor changes
- removed examples' and vignettes' dependencies on qtl2 R package.
qtl2pleio 1.2.0
Major changes
- changed output of scan_pvl to be log10 likelihood, not log (natural base) likelihood. Thank you to @HongHe0123 for suggesting this.
Minor changes
- changed column name for tibble outputs to reflect log base 10 instead of log natural base.
qtl2pleio 1.1.0
Major changes
- rewrites (and deletions) of tibble helper functions
- major revisions to code in main vignette
Minor changes
- fixed CITATION after G3 publication
qtl2pleio 1.0.7
Major changes
- None
Minor changes
- fixed Description field of DESCRIPTION file per feedback from CRAN
qtl2pleio 1.0.6
Major changes
- None
Minor changes
- removed Additional_repositories field from DESCRIPTION
qtl2pleio 1.0.5
Major changes
- None
Minor changes
- added cran-comments.md file via devtools & added it to .Rbuildignore
qtl2pleio 1.0.4
Major changes
- None
Minor changes
- Added Additional_repositories field to DESCRIPTION file per https://cran.r-project.org/submit.html in preparation for CRAN submission.
- Added url for Jiang and Zeng 1995 GENETICS article, per https://cran.r-project.org/submit.html.
qtl2pleio 1.0.3
Major changes
- Revisions per peer review at Journal of Open Source Software
Minor changes
- None
qtl2pleio 0.1.3
Major changes
- Submitted paper.md to JOSS
Minor changes
- Minor updates to recla vignette to download precalculated founder allele dosages
qtl2pleio 0.1.2.9002
Major changes
- changed default behavior of
plot_pvlto not indicate univariate peak positions. - fixed CITATION file to tell users to cite Biorxiv preprint (following CITATION file format of rqtl/qtl2)
Minor changes
- Removed hex logo file from repo and deleted it from README
- revised paper.md in preparation for JOSS submission
Bug fixes
-
Re-created profile LOD plots for vignettes and README without indicating univariate peak positions.
-
Added line type arguments to
plot_pvl.
qtl2pleio 0.1.2.9001
Major changes
- added a vignette for HTCondor & bootstrap analysis
- updated README.Rmd and README.md (per suggestions & PR of @kbroman)
qtl2pleio 0.1.2.9000
Major changes
- added inst/CITATION file
- aligned ordering and names of arguments for both
boot_pvlandscan_pvl - added examples for
boot_pvl - added literature references to both
boot_pvlandscan_pvl
Bug fixes
- corrected typo in vignette
qtl2pleio 0.1.2
Major changes
- added tests & examples for
scan_pvl - changed output of
scan_pvlto a tibble - added
boot_nfunction for use in bootstrap analyses - started using covariates in calls to
calc_covs. Note that we still don't use genetic data when callingcalc_covs. - deprecated
calc_loglik_bvlmm
qtl2pleio 0.1.1
Major changes
- restructured
scan_pvlto allow for more than two phenotypes. Now output is a dataframe.
qtl2pleio 0.1.0
Major changes
- Added a
NEWS.mdfile to track changes to the package.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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