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.