Changed it so ancestry prediction function works with PLINK 1.9v
files. The default is that there are PLINK 1.9v files available. Users
can use the plink2format parameter if the data is in PLINK 2.0
format.
Added convert_to_vcf() function to convert vcf files to PLINK
format
Added parameter to ancestry function so user can use their own
trained classifier
added a parameter write_multiqc for functions relating to sample QC
to create reports compatible with multiQC
plinkQC 1.0.1
minor changes
Fixed a bug so that ancestry prediction function works when there
are phenotypes included in the input data.
plinkQC 1.0.0
major changes
Added a pre-trained random forest classifier to predict genomic
ancestry with the functions ancestry_prediction()
Added the new random forest classifier as a flag to
perIndividualQC() and cleanData() so the user can filter out selected
ancestries.
Updated check_relatedness() to run more efficiently. The function
now has a faster run-time and increased the number of samples retained
in edge cases.
minor changes
Added checkplink2 to return the correct path for plink v2
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
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)