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plinkQC
0.2.3
documentation
Step-by-step QC
Ancestry
HapMap III reference
1000 Genomes reference
news
functions
github
Changelog
Source:
NEWS.md
plinkQC 0.2.3
Unreleased
major changes
Enable return of overview plots as ggplot object (fixes
#6
in ab2e840f0f22ccdeb5317475698aa58e7eecd345 and 101e74e318752b2f8038330245d875f6afd5b57b)
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 1445a88d41d985e73ffdd161144229683f8352cd
Include check in case all samples fail perIndividual QC in 894acc1fa03dadfe0ad2028888142171bcc641eb and 04642246d18ed4eaac5b9d9a6931d1ecb08308e8)
Include checks for diagonal derived relationship estimates, and estimate data containing only related individuals; fixes
#11
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.
Contents
0.2.3
0.2.2
0.2.1
0.2.0
0.1.1
0.1.0