kinship.diagnostics {ASRgenomics} R Documentation

## Reports summary statistics, plots and filter options for a given kinship matrix K

### Description

It reports summary statistics, plots and allows for some filter options for diagonal and off-diagonal elements for a given kinship matrix. The input matrix can be a pedigree-based relationship matrix \boldsymbol{A}, a genomic relationship matrix \boldsymbol{G} or a hybrid relationship matrix \boldsymbol{H}. Individual names should be assigned to rownames and colnames.

### Usage

kinship.diagnostics(
K = NULL,
diagonal.thr.large = 1.2,
diagonal.thr.small = 0.8,
duplicate.thr = 0.95,
clean.diagonal = FALSE,
clean.duplicate = FALSE,
plots = TRUE,
sample.plot = 1,
message = TRUE
)


### Arguments

 K Input of a kinship matrix in full format (n \times n) (default = NULL). diagonal.thr.large A threshold value to flag large diagonal values (default = 1.2). diagonal.thr.small A threshold value to flag small diagonal values (default = 0.8). duplicate.thr A threshold value to flag possible duplicates. Any calculation larger than the threshold based on \boldsymbol{k}_{i,i}\mathbin{/}\sqrt{\boldsymbol{k}_{i,i} \times \boldsymbol{k}_{j,j}} is identified as a duplicate (default = 0.95). clean.diagonal If TRUE returns a kinship matrix filtered by values smaller than diagonal.thr.large and larger than diagonal.thr.small (default = FALSE). clean.duplicate If TRUE return a kinship matrix without the flagged duplicate individuals. All individuals involved are removed (default = FALSE). plots If TRUE generates graphical output of the diagonal and off-diagonal values of the kinship matrix (default = TRUE). sample.plot A numeric value between 0 and 1 indicating the proportion of the data points to be sampled for fast plotting of off-diagonal values. Note that for proportions other than 1, the method is not exact and low proportions are only recommended for large kinship matrices (default = 1). message If TRUE diagnostic messages are printed on screen (default = TRUE).

### Value

A list with the following elements:

• list.diagonal: a data frame with the list of flagged large or small diagonal values.

• list.duplicate: a data frame with the list of possible duplicates.

• clean.kinship: output of kinship matrix filtered without the flagged diagonal and/or duplicate individuals.

• plot.diagonal: histogram with the distribution of diagonal values from the kinship matrix.

• plot.offdiag: histogram with the distribution of off-diagonal values from kinship matrix.

### Examples

# Get G matrix.
G <- G.matrix(M = geno.apple, method = "VanRaden")$G # Diagnose G. G_summary <- kinship.diagnostics( K = G, diagonal.thr.large = 1.3, diagonal.thr.small = 0.7, clean.diagonal = TRUE, duplicate.thr = 0.8, clean.duplicate = TRUE, sample.plot = 0.50) ls(G_summary) dim(G_summary$clean.kinship)
G_summary$clean.kinship[1:5, 1:5] G_summary$list.duplicate
G_summary$list.diagonal G_summary$plot.diag
G_summary\$plot.offdiag



[Package ASRgenomics version 1.1.4 Index]