# plinkQC 1.1.0
## major changes
* Changed it so ancestry prediction function works with PLINK 1.9v files. The default is 
that there are PLINK 1.9v files available. Users can use the plink2format parameter if
the data is in PLINK 2.0 format.
* Added convert_to_vcf() function to convert vcf files to PLINK format 
* Added parameter to ancestry function so user can use their own trained classifier 
* added a parameter write_multiqc for functions relating to sample QC to create
reports compatible with multiQC

# plinkQC 1.0.1
## minor changes
* Fixed a bug so that ancestry prediction function works when there are phenotypes included in the input data.

# plinkQC 1.0.0
## major changes
* Added a pre-trained random forest classifier to predict genomic ancestry with the functions ancestry_prediction()
* Added the new random forest classifier as a flag to perIndividualQC() and cleanData() so the user can filter out selected ancestries.
* Updated check_relatedness() to run more 
efficiently. The function now has a faster run-time and increased the number of samples retained in edge cases. 

## minor changes
* Added checkplink2 to return the correct path for plink v2 

# plinkQC 0.3.4
## major changes
* Add flag for removing high LD regions and add option for user provided file,
allowing removal of high LD regions for non-human organisms; fix missing flag
[19bc569](https://github.com/meyer-lab-cshl/plinkQC/commit/19bc5697f80c4766d91c24d773337b8bf88a3e6f) and
[#42](https://github.com/meyer-lab-cshl/plinkQC/issues/42)
* Fixed failing data.no_failIDs.lmiss file in check_snp_missingness function
when failIDs were present
[86adc39](https://github.com/meyer-lab-cshl/plinkQC/commit/86adc39764ed6271e947d12063229be0e0189d12) and
[#43](https://github.com/meyer-lab-cshl/plinkQC/issues/43)

# plinkQC 0.3.3
## major changes
* Output all IBD estimates in `run_check_relatedness` not just fail IBD
estimates [d009da90](https://github.com/meyer-lab-cshl/plinkQC/commit/d009da90434a83cb4867881e3772b518d17dc2dd)
* Add midp modifier for --hwe and --hardy as recommended on [plink hwe documentation](https://www.cog-genomics.org/plink/1.9/filter#hwe) and discussed in issue [#27](https://github.com/meyer-lab-cshl/plinkQC/issues/27); [43230a6c](https://github.com/meyer-lab-cshl/plinkQC/commit/43230a6ce5f079b46c85b1a7a526213177db1f1b)
* Provide HapMap and 1000Genomes individual and population identifiers as default
for ancestry check functions; include optional color mapping for these reference
populations; raised in [#37](https://github.com/meyer-lab-cshl/plinkQC/issues/37), incorporated in [65cfcba](https://github.com/meyer-lab-cshl/plinkQC/commit/65cfcbaf5b0af3b1d3d4b710a8710331a39e0f6e)
* for all individual QC functions return data.frame with FID, IID and measure
used for filtering [#5](https://github.com/meyer-lab-cshl/plinkQC/issues/5)
incorporated in [295505b](https://github.com/meyer-lab-cshl/plinkQC/commit/295505bc2d2a6278539e1d078c338bcf3a128338)
* allow for user-supplied individual and marker filtering in perIndividualQC,
perMarkerQC and cleanData [#33](https://github.com/meyer-lab-cshl/plinkQC/issues/33)
* individual highlighting in perIndividualQC plots; several highlight modalities
(text/label, shape, color) [#38](https://github.com/meyer-lab-cshl/plinkQC/issues/38)


## minor changes
* Add checks in `cleanData` that can distinguish between miss-specified filters and non-failing samples [7432b1ee](https://github.com/meyer-lab-cshl/plinkQC/commit/7432b1ee880ad14c7a078f3a0379f7fdcff1684b); addresses issue [#31](https://github.com/meyer-lab-cshl/plinkQC/issues/31) 
* Add checks and tests in `check_snp_missingness`, `check_maf` and `check_hwe` 
in cases where all samples pass `perIndividualQC`.
[31ed6f65](https://github.com/meyer-lab-cshl/plinkQC/commit/31ed6f653902857a0a78ae723e786dd84d240b75); related to issue [#31](https://github.com/meyer-lab-cshl/plinkQC/issues/31) 
* Add checks and tests in `evaluate_check_sex` and `evaluate_check_het_imiss`
for all passing samples and accordingly, no fail samples label in plot.
[d071a43](https://github.com/meyer-lab-cshl/plinkQC/commit/d071a4341b0d4c40220b42f81c412da4d320b8ec)
* Update dropbox links and add note to vignette [9bae988](https://github.com/meyer-lab-cshl/plinkQC/commit/9bae9886dc637569698d883654fcf71486b6634e)
* additional plotting parameters for `evaluate_*` functions, controlling 
text and title sizes ([b38a348](https://github.com/meyer-lab-cshl/plinkQC/commit/b38a348da0a4dd60860543b2d53c4de1df058a54),
[f25b8d0](https://github.com/meyer-lab-cshl/plinkQC/commit/f25b8d05bc3462228afb26bb1caec8d829bf7fca))


# plinkQC 0.3.2
## minor changes
* Add checks and tests in `evaluate_check_ancestry` for missing non-reference samples
[5c03971](https://github.com/meyer-lab-cshl/plinkQC/commit/5c03971b92341b5a8cb26a1d5f2e37d637f5cbd7)
* Clarified tutorials:
  * R internal file.copy instead of systems `cp` command to make run on windows: [6c91ef3](https://github.com/meyer-lab-cshl/plinkQC/commit/6c91ef3368f601658967f88bc20db94a28307fce),
  fixes [#26](https://github.com/meyer-lab-cshl/plinkQC/issues/26) 
  * Add additional filter for A->T, C->G variants as suggested in [#24](https://github.com/meyer-lab-cshl/plinkQC/issues/24); [11e0375](https://github.com/meyer-lab-cshl/plinkQC/commit/11e03756852215915310a836d2e73dbcedf12bfc)
* Fixed plotting issues in PCA plot of ancestry check:
  * allow for supplying names of European reference population [ae09e64](https://github.com/meyer-lab-cshl/plinkQC/commit/ae09e64ee2eaeb8337b60b24b126a9c049d6315f)
  * provide argument to specify number of populations per legend row [c7fe85d](https://github.com/meyer-lab-cshl/plinkQC/commit/c7fe85d555c256bf8be3843803ff1cc445f7898f)
  * Ensure correct ordering of population colors when reference population is not HapMap [86275b7](https://github.com/meyer-lab-cshl/plinkQC/commit/86275b7c281835681f38ab16672db61c288cfed9)

# plinkQC 0.3.1
## minor changes

* Fixed dead links in vignettes (caused by migration of repository): [da987d8](https://github.com/meyer-lab-cshl/plinkQC/commit/da987d8f225aa6aca0596b9c4f6a2484b102bdb6)
* Added note about chrY in Hapmap data (vignette): [e8afbb9](https://github.com/meyer-lab-cshl/plinkQC/commit/e8afbb9842ed9421461a8114ac0a00f7955cf0c0)
* Added note about recommended use of plink1.9 (vs 2.0):
[b69d3d7](https://github.com/meyer-lab-cshl/plinkQC/commit/b69d3d71d23e9b161176a635fcb2b5a2b524591f)

# plinkQC 0.3.0
## major changes
* Relationship filter can handle more complicated relationship scenarios as
  observed in plant genotype sets (fixed [#11](https://github.com/meyer-lab-cshl/plinkQC/issues/11))
* code moved to the meyer-lab repository: https://github.com/meyer-lab-cshl/plinkQC

# plinkQC 0.2.3
## major changes
* Enable return of overview plots as ggplot object
  (fixes  [#6](https://github.com/meyer-lab-cshl/plinkQC/issues/6) in [ab2e840](https://github.com/meyer-lab-cshl/plinkQC/commit/ab2e840f0f22ccdeb5317475698aa58e7eecd345) and
  [101e74e](https://github.com/meyer-lab-cshl/plinkQC/commit/101e74e318752b2f8038330245d875f6afd5b57b))
* Relationship filter now deals with more complicated relationship scenarios as
  observed in plant genotype sets (addresses [#11](https://github.com/meyer-lab-cshl/plinkQC/issues/11))

## minor changes
* give user option to choose maf threshold for relatedness filtering (relates to
   [#3](https://github.com/meyer-lab-cshl/plinkQC/issues/3))

## bug fixes
* Include check for zero related individuals fixing  [#3](https://github.com/meyer-lab-cshl/plinkQC/issues/3) in
  [1445a88](https://github.com/meyer-lab-cshl/plinkQC/commit/1445a88d41d985e73ffdd161144229683f8352cd)
* Include check in case all samples fail perIndividual QC in
   [894acc1](https://github.com/meyer-lab-cshl/plinkQC/commit/894acc1fa03dadfe0ad2028888142171bcc641eb) and
   [0464224](https://github.com/meyer-lab-cshl/plinkQC/commit/04642246d18ed4eaac5b9d9a6931d1ecb08308e8))
* Include checks for diagonal derived relationship estimates, and estimate data
  containing only related individuals; addresses  [#11](https://github.com/meyer-lab-cshl/plinkQC/issues/11)
* Fix command for genotype conversion in 1000Genomes vignette, addressing issue
   [#10](https://github.com/meyer-lab-cshl/plinkQC/issues/10)
* fix missing rownames error for overviewPerIndividualQC, when relatedness check
  was included (issue [#16](https://github.com/meyer-lab-cshl/plinkQC/issues/16), [fc7a38b](https://github.com/meyer-lab-cshl/plinkQC/commit/fc7a38b1f2b345d9c6c5d69f5dcf0bc57a857f62))
* fix vignette mismatch (issue [#16](https://github.com/meyer-lab-cshl/plinkQC/issues/16), [09dcd59](https://github.com/meyer-lab-cshl/plinkQC/commit/09dcd59e77178b35747aae81a5c1988712e20de9))

# plinkQC 0.2.2
## minor changes
* Fix IDs written to fail.IDs file: previous versions wrote IID,IID, now fixed
to FID, IID (fixes [#2](https://github.com/meyer-lab-cshl/plinkQC/issues/2)).

# plinkQC 0.2.1
## minor changes
* Fix path check bug in checkPlink
* Include test data in build!

# plinkQC 0.2.0
## major changes
* All system calls to plink are conducted with sys::exec_wait - this should
solve platform dependent issues, mainly compatibility with windows.
* Make path construction compatible with windows.
* path2plink now requires full path to plink executable, no tilde expansion or
simple pointer to directory supported.
* Fix bug in return of cleanData function: list now contains keep and fail IDs.
* Fix bug in return of maf computation: if fail.IDs does not exist, set
  fail_samples to zero.

## minor changes
* IBD-fail.IDs now saved without column names to be consistent with other
xxx-fail.IDs files.
* Include additional progress messages in cleanData()
* Remove default double-specification of mafTh and macTh
* use checkPlink to return correct path2plink and export to make checkPlink
directly accesible to user.


# plinkQC 0.1.1
## major changes
* run_check_relatedness will only save IBD estimates of individuals whose
estimates are higher than the threshold.

## minor changes
* Fix examples in vignettes 1000 Genomes and HapMap III reference.
* Change file access in function examples
* Add additional checks in check_ancestry and fix missing refSamplesFile test


# plinkQC 0.1.0

* Added a `NEWS.md` file to track changes to the package.



