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Resubmission

major changes

  • Enable return of overview plots as ggplot object (fixes #6 in ab2e840f0f22ccdeb5317475698aa58e7eecd345 and 101e74e318752b2f8038330245d875f6afd5b57b)
  • Relationship filter now deals with more complicated relationship scenarios as observed in plant genotype sets (fixed #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 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
  • Fix command for genotype conversion in 1000Genomes vignette, addressing issue #10
  • fix missing rownames error for overviewPerIndividualQC, when relatedness check was included (issue #16, fc7a38b1f2b345d9c6c5d69f5dcf0bc57a857f62)

Test environments

  • local OS X install, R 3.6.1
  • ubuntu 14.04 (on travis-ci), R 3.6.1
  • win-builder (devel and release)

R CMD check results

0 errors | 0 warnings | 1 note

  • This is a new release.