pangemma/example, branch masterPanGEMMA: Genome-wide Efficient Mixed Model Association
http://git.genenetwork.org/pangemma/atom?h=master2018-03-07T02:50:25+00:00Added link to RCC workshop.2018-03-07T02:50:25+00:00Peter Carbonetto2018-03-07T02:50:25+00:00urn:sha1:678552c172e16b7964affe70404d40deb6e749bfAdded simulated phenotypes for HLC.2017-10-05T09:19:58+00:00Pjotr Prins2017-10-05T09:19:58+00:00urn:sha1:7b09fe8507962f20ccb1650b86408d40db1a0052
-n 1 2 3 13 are independent. The others depend on 3 and 13.
Tests and enforces added related to https://github.com/genetics-statistics/GEMMA/issues/782017-08-26T09:38:00+00:00Pjotr Prins2017-08-26T07:41:48+00:00urn:sha1:ea21ba73273891261ba2e4d0d85729f308c54d72Added more detailed description of -widv option following Xiang's description given in Issue #59.2017-08-21T16:37:49+00:00Peter Carbonetto2017-08-21T16:37:49+00:00urn:sha1:3a06aee66e89451f4705a6e54fb3256cbfa30e1aIssue 58, add tests for GSLv2 NaN's showing up with covariates2017-08-14T10:21:25+00:00Pjotr Prins2017-08-14T09:59:42+00:00urn:sha1:d9556d0aa21a084bd39f0188c88c8c3f09f71ab4
https://github.com/genetics-statistics/GEMMA/issues/58
LOCO is implemented in GEMMA for the BIMBAM format. Pass in the -loco2017-08-03T10:26:52+00:00Pjotr Prins2017-08-03T10:26:52+00:00urn:sha1:449d882a3b33ef81ef4f0127c3932b01fa796dbb
1 switch for LOCO of chromosome 1.
What are the use cases?
1. User runs vanilla GEMMA: all SNPs are considered input for GWA and K
2. User passes in -snps: all these SNPs are considered for GWA and K
3. User passes in -snps and -ksnps: All these SNPs are used for GWA,
Ksnps are used for K
4. User passes in -loco: SNPs are split by chromosome (GWA incl., K
excl.)
5. User passes in -snps, -gwasnps and -ksnps could mean that also GWA
is subset explicitely (nyi)
In all cases indicator_snp is honored and we get the most flexible way for
studying SNP combinations that can be passed in in different ways.
Overall added:
- various comments in source code
- tests in test framework inlc. fast-check
- NDEBUG compilation support in the Makefile
- -debug switch for GEMMA debug output
- debug.h which includes enforce functions which work like
assert. Unlike assert, enforce also works in release compilation
- -nind switch limit the number of individuals used
(trim_individuals for testing)
- enforcing tests of input files - e.g. are number of individuals correct
- checks for memory allocation - we should add more of those
- more checks for gsl results - we should add more of those
- replaced strtoken with regex as a first case. They should all be
replaced. strtoken is not thread safe, for one.
- introduced C++ iterators
- introduced C++ closure in BimBam LMM for cached processing
- more localized initialization of variables - makes for demonstratably
more correct code
- -ksnps adds snps into setKSnps
- -gwasnps adds snps into setGWASnps
- both sets are computed by -loco
- attempted to make the code easier to read
Spacing in demo.txt2017-07-09T09:04:25+00:00Pjotr Prins2017-07-09T09:04:25+00:00urn:sha1:7ff18ffdf85d3cb66564443bfa9b5f2836f60a25Removed src/Eigen; instead, Eigen C++ library is downloaded separately. See Issue #42 for tests performed.2017-05-27T21:07:07+00:00Peter Carbonetto2017-05-27T21:07:07+00:00urn:sha1:338bf7b7db8805515597d9e2d4b5dcbe2e40dfd1Putatively fixed -Wc++11-narrowing error in io.cpp (see Issue #24).2017-05-09T17:48:27+00:00Peter Carbonetto2017-05-09T17:48:27+00:00urn:sha1:f808355cd7abbadd2fbcc5ff471ba89a12205159version 0.95alpha2014-10-07T10:50:56+00:00xiangzhou2014-10-07T10:50:56+00:00urn:sha1:d150a16026a013edf91376213931a9d89d559713