getSparseLD: Extract Sparse Linkage Disequilibrium (LD) Information

In psoerensen/qgg: Statistical Tools for Quantitative Genetic Analyses

Extract Sparse Linkage Disequilibrium (LD) Information

Description

Retrieves and formats linkage disequilibrium (LD) data from binary files based on a specified chromosome and LD threshold. It provides options for returning the data in sparse or dense format.

Usage

getSparseLD(
  Glist = NULL,
  chr = NULL,
  r2 = 0,
  onebased = FALSE,
  rsids = NULL,
  format = "sparse"
)

Arguments

Glist	A list containing details such as the LD file path, msize, rsids for LD.
chr	A numeric value representing the chromosome for which LD data is to be extracted.
r2	A numeric value specifying the LD threshold for extraction. Default is 0.
onebased	A logical value indicating whether indices are one-based (default) or zero-based.
rsids	A vector of rsids for which the LD data needs to be extracted in dense format. Default is NULL.
format	A character string specifying the format of the result, either "sparse" (default) or "dense".

Value

If 'format' is "sparse", a list with two components: 'indices' and 'values'. Each component is a list of length equal to the number of rsids in the specified chromosome. If 'format' is "dense", a matrix with rows and columns named after the rsids is returned.

psoerensen/qgg documentation built on March 9, 2024, 10:02 p.m.