plinkQC (version 0.2.2)

check_ancestry: Identification of individuals of divergent ancestry

Description

Runs and evaluates results of plink --pca on merged genotypes from individuals to be QCed and individuals of reference population of known genotypes. Currently, check ancestry only supports automatic selection of individuals of European descent. It uses information from principal components 1 and 2 returned by plink --pca to find the center of the European reference samples (mean(PC1_europeanRef), mean(PC2_europeanRef). It then computes the maximum Euclidean distance (maxDist) of the European reference samples from this centre. All study samples whose Euclidean distance from the centre falls outside the circle described by the radius r=europeanTh* maxDist are considered non-European and their IDs are returned as failing the ancestry check. check_ancestry creates a scatter plot of PC1 versus PC2 colour-coded for samples of the reference populations and the study population.

Usage

check_ancestry(indir, name, qcdir = indir, prefixMergedDataset,
  europeanTh = 1.5, refSamples = NULL, refColors = NULL,
  refSamplesFile = NULL, refColorsFile = NULL, refSamplesIID = "IID",
  refSamplesPop = "Pop", refColorsColor = "Color",
  refColorsPop = "Pop", studyColor = "#2c7bb6",
  run.check_ancestry = TRUE, interactive = FALSE, verbose = verbose,
  path2plink = NULL, showPlinkOutput = TRUE)

Arguments

indir

[character] /path/to/directory containing the basic PLINK data files name.bim, name.bed, name.fam files.

name

[character] prefix of plink files, i.e. name.bed, name.bim, name.fam.

qcdir

[character] /path/to/directory where prefixMergedDataset.eigenvec results as returned by plink --pca should be saved. Per default qcdir=indir. If run.check_ancestry is FALSE, it is assumed that plink --pca prefixMergedDataset has been run and qcdir/prefixMergedDataset.eigenvec exists.User needs writing permission to qcdir.

prefixMergedDataset

[character] Prefix of merged dataset (study and reference samples) used in plink --pca, resulting in prefixMergedDataset.eigenvec.

europeanTh

[double] Scaling factor of radius to be drawn around center of European reference samples, with study samples inside this radius considered to be of European descent and samples outside this radius of non-European descent. The radius is computed as the maximum Euclidean distance of European reference samples to the centre of European reference samples.

refSamples

[data.frame] Dataframe with sample identifiers [refSamplesIID] corresponding to IIDs in prefixMergedDataset.eigenvec and population identifier [refSamplesPop] corresponding to population IDs [refColorsPop] in refColorsfile/refColors. Either refSamples or refSamplesFile have to be specified.

refColors

[data.frame, optional] Dataframe with population IDs in column [refColorsPop] and corresponding colour-code for PCA plot in column [refColorsColor]. If not provided and is.null(refColorsFile) default colors are used.

refSamplesFile

[character] /path/to/File/with/reference samples. Needs columns with sample identifiers [refSamplesIID] corresponding to IIDs in prefixMergedDataset.eigenvec and population identifier [refSamplesPop] corresponding to population IDs [refColorsPop] in refColorsfile/refColors.

refColorsFile

[character, optional] /path/to/File/with/Population/Colors containing population IDs in column [refColorsPop] and corresponding colour-code for PCA plot in column [refColorsColor].If not provided and is.null(refColors) default colors for are used.

refSamplesIID

[character] Column name of reference sample IDs in refSamples/refSamplesFile.

refSamplesPop

[character] Column name of reference sample population IDs in refSamples/refSamplesFile.

refColorsColor

[character] Column name of population colors in refColors/refColorsFile

refColorsPop

[character] Column name of reference sample population IDs in refColors/refColorsFile.

studyColor

[character] Colour to be used for study population.

run.check_ancestry

[logical] Should plink --pca be run to determine principal components of merged dataset; if FALSE, it is assumed that plink --pca has been run successfully and qcdir/prefixMergedDataset.eigenvec is present; check_ancestry will fail with missing file error otherwise.

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_ancestry) via ggplot2::ggsave(p=p_ancestry, other_arguments) or pdf(outfile) print(p_ancestry) dev.off().

verbose

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

path2plink

[character] Absolute path to PLINK executable (https://www.cog-genomics.org/plink/1.9/) i.e. plink should be accesible as path2plink -h. The full name of the executable should be specified: for windows OS, this means path/plink.exe, for unix platforms this is path/plink. If not provided, assumed that PATH set-up works and PLINK will be found by exec_wait('plink').

showPlinkOutput

[logical] If TRUE, plink log and error messages are printed to standard out.

Value

Named [list] with i) fail_ancestry, containing a [data.frame] with FID and IID of non-European individuals and ii) p_ancestry, a ggplot2-object 'containing' a scatter plot of PC1 versus PC2 colour-coded for samples of the reference populations and the study population, which can be shown by print(p_ancestry).

Examples

# NOT RUN {
indir <- system.file("extdata", package="plinkQC")
name <- "data"
fail_ancestry <- check_ancestry(indir=indir, name=name,
refSamplesFile=paste(indir, "/HapMap_ID2Pop.txt",sep=""),
refColorsFile=paste(indir, "/HapMap_PopColors.txt", sep=""),
prefixMergedDataset="data.HapMapIII", interactive=FALSE,
run.check_ancestry=FALSE)
# }