GGoutlieR (version 1.0.2)

ggoutlier: Identify outliers with unusual geo-genetic patterns

Description

This function is used to identify outliers with unusual geo-genetic patterns using the KNN approach. For the details of the outlier detection approach, please see Chang and Schmid 2023 (doi:https://doi.org/10.1101/2023.04.06.535838)

Usage

ggoutlier(
  geo_coord,
  gen_coord,
  pgdM = NULL,
  method = c("geneticKNN", "geoKNN", "composite"),
  K = NULL,
  k_geneticKNN = NULL,
  k_geoKNN = NULL,
  klim = c(3, 50),
  make_fig = FALSE,
  plot_dir = ".",
  w_geo = 1,
  w_genetic = 2,
  p_thres = 0.05,
  s = 100,
  min_nn_dist = 100,
  cpu = 1,
  geneticKNN_output = NULL,
  geoKNN_output = NULL,
  verbose = TRUE,
  multi_stages = TRUE,
  maxIter = NULL,
  keep_all_stg_res = FALSE,
  warning_minR2 = 0.9
)

Value

an object of `list`. If you set `method = "composite"`, `ggoutlier` will return a nested `list` with two subsidiary `list` which are `"geneticKNN_result"` and `"geoKNN_result"`. Each subsidiary list includes five items: `statistics` is a `data.frame` consisting of the D_geography ("Dgeo") or D_genetics ("Dg") values, p values and a column of logic values showing if a sample is an outlier or not. `threshold` is a `data.frame` recording the significance threshold. `gamma_parameter` is a vector recording the parameter of the heuristic Gamma distribution. `knn_index` and `knn_name` are a `data.frame` recording the K nearest neighbors of each sample. The subsidiary list `geneticKNN_result` has an additional item called `"scalar"`, which records the value of geographical distance scalar used in the computation. If you set `method = "geneticKNN"`, or `method = "geoKNN"`, `ggoutlier` will return a `list` respectively corresponding to `"geneticKNN_result"` or `"geoKNN_result"`.

Arguments

geo_coord

matrix or data.frame with two columns. The first column is longitude and the second one is latitude.

gen_coord

matrix. A matrix of "coordinates in a genetic space". Users can provide ancestry coefficients or eigenvectors for calculation. If, for example, ancestry coefficients are given, each column corresponds to an ancestral population. Samples are ordered in rows as in `geo_coord`.

pgdM

matrix. A pairwise genetic distance matrix. Users can provide a customized genetic distance matrix with this argument. Samples are ordered in rows and columns as in the rows of `geo_coord`. The default of `pgdM` is `NULL`. If `pgdM` is not provided, a genetic distance matrix will be calculated from `gen_coord`.

method

string. The method to run `GGoutlieR`. It can be `"composite"`, `"geneticKNN"`, or `"geoKNN"`.

K

integer. Number of the nearest neighbors. If `K` is not `NULL`, the value will pass to `k_geneticKNN` and `k_geoKNN`.

k_geneticKNN

integer. Number of the nearest neighbors in a genetic space. The default is `NULL`. The `ggoutlier` will search the optimal K if `k_geneticKNN = NULL`.

k_geoKNN

integer. Number of the nearest neighbors in a geographical space. the default is `NULL`. The `ggoutlier` will search the optimal K if `k_geoKNN = NULL`.

klim

vector. A range of K to search for the optimal number of nearest neighbors. The default is `klim = c(3, 50)`

make_fig

logic. If `make_fig = TRUE`, plots for diagnosing GGoutlieR analysis will be generated and saved to `plot_dir`. The default is `FALSE`

plot_dir

string. The path to save plots

w_geo

numeric. A value controlling the power of distance weight in geographical KNN prediction.

w_genetic

numeric. A value controlling the power of distance weight in genetic KNN prediction.

p_thres

numeric. A significance level

s

integer. A scalar of geographical distance. The default `s=100` scales the distance to a unit of 0.1 kilometer.

min_nn_dist

numeric. A minimal geographical distance for searching KNNs. Neighbors of a focal sample within this distance will be excluded from the KNN searching procedure.

cpu

integer. Number of CPUs to use for searching the optimal K.

geneticKNN_output

output of `ggoutlier_geneticKNN`. Users can use this argument if running `ggoutlier_geneticKNN` in advance.

geoKNN_output

output of `ggoutlier_geoKNN`. Users can use this argument if running `ggoutlier_geoKNN` in advance.

verbose

logic. If `verbose = FALSE`, `ggoutlier` will suppress printout messages.

multi_stages

logic. A multi-stage test will be performed if is `TRUE` (the default is `TRUE`).

maxIter

numeric. Maximal iteration number of multi-stage KNN test.

keep_all_stg_res

logic. Results from all iterations of the multi-stage test will be retained if it is`TRUE`. (the default is `FALSE`)

warning_minR2

numeric. The prediction accuracy of KNN is evaluated as R^2 to assess the violation of isolation-by-distance expectation. If any R^2 is larger than `warning_minR2`, a warning message will be reported at the end of your analysis.

Examples

library(GGoutlieR)
data("ipk_anc_coef") # get ancestry coefficients
data("ipk_geo_coord") # get geographical coordinates


#DON'T RUN: this analysis will take a few minutes
if (FALSE) {
ggoutlier_example <-
                 ggoutlier(geo_coord = ipk_geo_coord,
                           gen_coord = ipk_anc_coef,
                           klim = c(3,6),
                           p_thres = 0.01,
                           cpu = 2,
                           method = "composite",
                           verbose = FALSE,
                           min_nn_dist = 1000,
                           multi_stages = FALSE)

head(summary_ggoutlier(ggoutlier_example)) # get a summary table
}