Changelog

Source: NEWS.md

plinkQC 0.3.4 2021-07-15

major changes

  • 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

plinkQC 0.3.3 2021-02-08

major changes

  • 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

minor changes

  • 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)

plinkQC 0.3.2 2020-07-07

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

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 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.

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.