NEWS.md

In plinkQC: Genotype Quality Control with 'PLINK'

plinkQC 0.3.4

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

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

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

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

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

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

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

minor changes

• Fix path check bug in checkPlink
• Include test data in build!

plinkQC 0.2.0

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

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

• Added a NEWS.md file to track changes to the package.

plinkQC documentation built on July 15, 2021, 5:07 p.m.