plinkQC (version 0.2.2)

evaluate_check_relatedness: Evaluate results from PLINK IBD estimation.

Description

Evaluates and depicts results from plink --genome on the LD pruned dataset (via run_check_relatedness or externally conducted IBD estimation). plink --genome calculates identity by state (IBS) for each pair of individuals based on the average proportion of alleles shared at genotyped SNPs. The degree of recent shared ancestry, i.e. the identity by descent (IBD) can be estimated from the genome-wide IBS. The proportion of IBD between two individuals is returned by --genome as PI_HAT. evaluate_check_relatedness finds pairs of samples whose proportion of IBD is larger than the specified highIBDTh. Subsequently, for pairs of individual that do not have additional relatives in the dataset, the individual with the greater genotype missingness rate is selected and returned as the individual failing the relatedness check. For more complex family structures, the unrelated individuals per family are selected (e.g. in a parents-offspring trio, the offspring will be marked as fail, while the parents will be kept in the analysis). evaluate_check_relatedness depicts all pair-wise IBD-estimates as histograms stratified by value of PI_HAT.

Usage

evaluate_check_relatedness(qcdir, name, highIBDTh = 0.1875,
  imissTh = 0.03, interactive = FALSE, verbose = FALSE)

Arguments

qcdir

[character] path/to/directory/with/QC/results containing name.imiss and name.genome results as returned by plink --missing and plink --genome.

name

[character] Prefix of PLINK files, i.e. name.bed, name.bim, name.fam, name.genome and name.imiss.

highIBDTh

[double] Threshold for acceptable proportion of IBD between pair of individuals.

imissTh

[double] Threshold for acceptable missing genotype rate in any individual; has to be proportion between (0,1)

interactive

[logical] Should plots be shown interactively? When choosing this option, make sure you have X-forwarding/graphical interface available for interactive plotting. Alternatively, set interactive=FALSE and save the returned plot object (p_IBD() via ggplot2::ggsave(p=p_IBD, other_arguments) or pdf(outfile) print(p_IBD) dev.off().

verbose

[logical] If TRUE, progress info is printed to standard out.

Value

a named [list] with i) fail_high_IBD containing a [data.frame] of IIDs and FIDs of individuals who fail the IBDTh in columns FID1 and IID1. In addition, the following columns are returned (as originally obtained by plink --genome): FID2 (Family ID for second sample), IID2 (Individual ID for second sample), RT (Relationship type inferred from .fam/.ped file), EZ (IBD sharing expected value, based on just .fam/.ped relationship), Z0 (P(IBD=0)), Z1 (P(IBD=1)), Z2 (P(IBD=2)), PI_HAT (Proportion IBD, i.e. P(IBD=2) + 0.5*P(IBD=1)), PHE (Pairwise phenotypic code (1, 0, -1 = AA, AU, and UU pairs, respectively)), DST (IBS distance, i.e. (IBS2 + 0.5*IBS1) / (IBS0 + IBS1 + IBS2)), PPC (IBS binomial test), RATIO (HETHET : IBS0 SNP ratio (expected value 2)). and ii) failIDs containing a [data.frame] with individual IDs [IID] and family IDs [FID] of individuals failing the highIBDTh iii) p_IBD, a ggplot2-object 'containing' all pair-wise IBD-estimates as histograms stratified by value of PI_HAT, which can be shown by print(p_IBD).

Details

Both run_check_relatedness and evaluate_check_relatedness can simply be invoked by check_relatedness.

For details on the output data.frame fail_high_IBD, check the original description on the PLINK output format page: https://www.cog-genomics.org/plink/1.9/formats#genome.

Examples

# NOT RUN {
qcdir <- system.file("extdata", package="plinkQC")
name <- 'data'
# }
# NOT RUN {
relatednessQC <- evaluate_check_relatedness(qcdir=qcdir, name=name,
interactive=FALSE)
# }