tagSNP {hscovar}

tagSNP

Description

Grouping of markers depending on correlation structure

Usage

tagSNP(mat, threshold = 0.8)

Arguments

mat

(p x p) correlation matrix

threshold

lower value of correlation considered for grouping

Details

Grouping of markers is based on the correlation matrix. Apart from this, the strategy for grouping is similar to Carlson et al. (2004). A representative marker is suggested for each group.

Value

list (LEN number of groups) of lists (LEN 2); marker names correspond to column names of mat

snps

vector of marker IDs in group

tagsnp

representative marker suggested for this group

References

Carlson, Eberle, Rieder, Yi, Kruglyak & Nickerson (2004) Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. American Journal of Human Genetics 74:106-120.

Wittenburg, Doschoris, Klosa (2021) Grouping of genomic markers in populations with family structure BMC Bioinformatics 22:79. doi: 10.1186/s12859-021-04010-0

Examples

  ### 1: INPUT DATA
  data(testdata)
  ### 2: COVARIANCE/CORRELATION MATRIX
  corrmat <- CovMat(matLD, H.sire, 100, pos.chr, corr = TRUE)
  ### 3: TAGSNPS FROM CORRELATION MATRIX
  bin <- tagSNP(corrmat$R)
  bin <- tagSNP(corrmat$R, 0.5)
  as.numeric(unlist(rlist::list.select(bin, tagsnp)))