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plinkQC
0.3.2
documentation
Step-by-step QC
Ancestry
HapMap III reference
1000 Genomes reference
news
functions
github
Changelog
Source:
NEWS.md
plinkQC 0.3.2
Unreleased
minor changes
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
plinkQC 0.3.1
Unreleased
minor changes
Fixed dead links in vignettes (caused by migration of repository):
da987d8
Added note about chrY in Hapmap data (vignette):
e8afbb9
Added note about recommended use of plink1.9 (vs 2.0):
b69d3d7
plinkQC 0.3.0
2019-10-19
major changes
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
plinkQC 0.2.3
2019-09-25
major changes
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
)
minor changes
give user option to choose maf threshold for relatedness filtering (relates to
#3
)
bug fixes
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
)
plinkQC 0.2.2
2019-06-19
minor changes
Fix IDs written to fail.IDs file: previous versions wrote IID,IID, now fixed to FID, IID (fixes
#2
).
plinkQC 0.2.1
2019-03-01
minor changes
Fix path check bug in checkPlink
Include test data in build!
plinkQC 0.2.0
2018-11-09
major changes
All system calls to plink are conducted with sys::exec_wait - this should solve platform dependent issues, mainly comptatibility 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
2018-11-06
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
2018-11-04
Added a
NEWS.md
file to track changes to the package.
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