NEWS

plinkQC 0.3.4 (2021-07-15)

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 and #42
Fixed failing data.no_failIDs.lmiss file in check_snp_missingness function when failIDs were present 86adc39 and #43

Output all IBD estimates in run_check_relatedness not just fail IBD estimates d009da90
Add midp modifier for --hwe and --hardy as recommended on plink hwe documentation and discussed in issue #27; 43230a6c
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, incorporated in 65cfcba
for all individual QC functions return data.frame with FID, IID and measure used for filtering #5 incorporated in 295505b
allow for user-supplied individual and marker filtering in perIndividualQC, perMarkerQC and cleanData #33
individual highlighting in perIndividualQC plots; several highlight modalities (text/label, shape, color) #38

Add checks in cleanData that can distinguish between miss-specified filters and non-failing samples 7432b1ee; addresses issue #31
Add checks and tests in check_snp_missingness, check_maf and check_hwe in cases where all samples pass perIndividualQC. 31ed6f65; related to issue #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
Update dropbox links and add note to vignette 9bae988
additional plotting parameters for evaluate_* functions, controlling text and title sizes (b38a348, f25b8d0)

Add checks and tests in evaluate_check_ancestry for missing non-reference samples 5c03971
Clarified tutorials:
- R internal file.copy instead of systems cp command to make run on windows: 6c91ef3, fixes #26
- Add additional filter for A->T, C->G variants as suggested in #24; 11e0375
Fixed plotting issues in PCA plot of ancestry check:
- allow for supplying names of European reference population ae09e64
- provide argument to specify number of populations per legend row c7fe85d
- Ensure correct ordering of population colors when reference population is not HapMap 86275b7

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

Enable return of overview plots as ggplot object (fixes #6 in ab2e840 and 101e74e)
Relationship filter now deals with more complicated relationship scenarios as observed in plant genotype sets (addresses #11)

give user option to choose maf threshold for relatedness filtering (relates to #3)

Include check for zero related individuals fixing #3 in 1445a88
Include check in case all samples fail perIndividual QC in 894acc1 and 0464224)
Include checks for diagonal derived relationship estimates, and estimate data containing only related individuals; addresses #11
Fix command for genotype conversion in 1000Genomes vignette, addressing issue #10
fix missing rownames error for overviewPerIndividualQC, when relatedness check was included (issue #16, fc7a38b)
fix vignette mismatch (issue #16, 09dcd59)

Fix IDs written to fail.IDs file: previous versions wrote IID,IID, now fixed to FID, IID (fixes #2).

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.

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.

run_check_relatedness will only save IBD estimates of individuals whose estimates are higher than the threshold.