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)
major changes
run_check_relatednessnot just fail IBD estimates d009da90minor changes
cleanDatathat can distinguish between miss-specified filters and non-failing samples 7432b1ee; addresses issue #31check_snp_missingness,check_mafandcheck_hwein cases where all samples passperIndividualQC. 31ed6f65; related to issue #31evaluate_check_sexandevaluate_check_het_imissfor all passing samples and accordingly, no fail samples label in plot. d071a43evaluate_*functions, controlling text and title sizes (b38a348, f25b8d0)