admixr - admixr 0.9.1

• Added executable examples to each function.
• First official CRAN release! 🎉

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Published by bodkan about 6 years ago

admixr - admixr 0.9.0

• New prototype implementation of exhaustive search of qpAdm models through rotation of sources and outgroups (qpAdm_rotation()).
• New tutorial describing the qpAdm_rotation() procedure.
• Fixed broken regex parsing of qpWave log files in some cases.
• Added type checking to a couple of functions (not all wrappers type checked yet).

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Published by bodkan about 6 years ago

admixr - admixr 0.8.7

• qpAdm proportions table now shows p-values and SNP counts (both for overall analysis but also for the target sample).

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Published by bodkan about 6 years ago

admixr - admixr 0.8.6

• Satisfying further checks on various testing servers.
• Cleanup of tests and imports.
• Updated license.
• Prepared for the first CRAN submission.

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Published by bodkan about 6 years ago

admixr -

- R
Published by bodkan about 6 years ago

admixr - admixr 0.8.3

• Updated license.

- R
Published by bodkan about 6 years ago

admixr - admix 0.8.2

• Expanded some tests.
• Prepared for the first CRAN submission.

- R
Published by bodkan about 6 years ago

admixr - admixr 0.8.1

• Fixed a minor bug in single-source qpAdm analyses. The package now detects this and correctly handles missing "subsets/patterns" information.

- R
Published by bodkan about 6 years ago

admixr - admixr 0.8.0

• New function loginfo() which operates on any output object from an admixr wrapper and shows the full log output (the “log file” in ADMIXTOOLS jargon) associated with the analysis. It also has options for saving the log file to a permanent location and to only show a log file for a target sample of interest (relevant for qpAdm analyses with multiple targets at once).

• admixr can now (hopefully) detect broken/truncated output files generated by ADMIXTOOLS whenever there is some fatal issue with an analysis. The package should now detect this and inform the user.

• Removed qpAdm argument details - the user will always want to see the full analysis summary so this option is redundant. It is still kept in qpWave - for now, until I figure out how useful the full output actually is. Given the implementation of loginfo() above, we might remove the argument from qpWave too at some point soon.

• The function download_data() fetches data from a more stable location.

- R
Published by bodkan about 6 years ago

admixr - admixr 0.7.1

• Parse admixture proportions from the "best coefficients" line of the qpAdm output file.

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Published by bodkan over 7 years ago

admixr - admixr 0.7.0

• Fixed handling of warnings when dealing with duplicated populations.
• 9s are now replaced with NAs in readgeno() and writegeno(), which makes it more convenient to write custom analytic code working on data.frames.
• Renamed qpAdm() output elements and changed its function signature.

- R
Published by bodkan over 7 years ago

admixr - admixr 0.6.3

• Rename keep_transversions() to transversions_only(). The old function is now deprecated.
• print.EIGENSTRAT() now uses a pre-calculated numbers of removed/remaining sites, instead of calculating them each and every time.
• Printing EIGENSTRAT objects now also shows “group” and “exclude” modifiers only if present.

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Published by bodkan over 7 years ago

admixr - admixr v0.6.2

• read_output() made public.
• Fixed issues with parsing of mis-formatted ind files (tabs at the ends of lines etc.).

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Published by bodkan over 7 years ago

admixr - admixr v0.6.1

It turned out that dragging along Rcpp and Boost dependencies just for the VCF -> EIGENSTRAT conversion function causes unnecessary complications in the installation process. It’s not worth having it in the package if it would be used only by a small fraction of potential users.

This function has been removed and the vcf2eigenstrat program is maintained in its own repository.

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Published by bodkan over 7 years ago

admixr - admixr v0.6

• Conversion of VCF to EIGENSTRAT format is now implemented in C++ and should be approximately infinitely faster than the old conversion function written in pure R.
• Conversion of EIGENSTRAT into VCF has been removed.

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Published by bodkan over 7 years ago

admixr - admixr v0.5

• Added full implementations of qpWave() and qpAdm() functions.
• filter_bed() now implemented simply by calling bedtools in the background. This turned out to be way faster and memory efficient than the previous data.table-based solution.

- R
Published by bodkan over 7 years ago

admixr - admixr 0.4.1

• Fixed missing group_labels() update.
• Removed the huge built-in data set. Implemented download_data() function that fetches the example data set from the web.

- R
Published by bodkan almost 8 years ago

admixr - admixr 0.4

• The package now has a tutorial vignette describing the main functionality.
• Simple SNP dataset is now included with the package.
• The API of many utility functions has been simplified and their internals re-written.
• filter_sites is now implemented using data.table and allows overlap with an arbitrary BED file.

- R
Published by bodkan almost 8 years ago

admixr - admixr 0.3

• All wrappers have been given simpler names (qpDstat() -> d(), qpF4ratio() -> f4ratio(), etc).
• F4 statistic can now be calculated using a separate f4() function (f4mode parameter remains in the d() function though, as f4() calls d() internally).
• All tests are performed on Travis CI using installed and compiled ADMIXTOOLS software.
• Changed names of function arguments of qpAdm and output directory argument of all wrappers.

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Published by bodkan almost 8 years ago

admixr - admixr 0.2

The package now includes qpAdm functionality.

Formal tests for all implemented wrapper functions have been implemented.

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Published by bodkan almost 8 years ago

admixr - admixr 0.1

Implemented

• D statistic as qpDstat,
• f4 statistic as qpDstat(f4mode = TRUE),
• f4-ratio statistic as qpF4Ratio,
• f3 statistic as qp3Pop.

These functions should be usable without any issues.

- R
Published by bodkan over 8 years ago