makeSparseMatrix: Make a sparse matrix from a dense matrix or a table of...

In UW-GAC/GENESIS: GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness

Make a sparse matrix from a dense matrix or a table of pairwise values

Description

makeSparseMatrix is used to create a sparse block-diagonal matrix from a dense matrix or a table of pairwise values, using a user-specified threshold for sparsity. An object of class Matrix will be returned. A sparse matrix may be useful for fitting the association test null model with fitNullModel when working with very large sample sizes.

Usage

## S4 method for signature 'data.table'
makeSparseMatrix(x, thresh = NULL, sample.include = NULL, diag.value = NULL,
                 verbose = TRUE)
## S4 method for signature 'data.frame'
makeSparseMatrix(x, thresh = NULL, sample.include = NULL, diag.value = NULL, 
                 verbose = TRUE)
## S4 method for signature 'matrix'
makeSparseMatrix(x, thresh = 2^(-11/2), sample.include = NULL, diag.value = NULL, 
                 verbose = TRUE)
## S4 method for signature 'Matrix'
makeSparseMatrix(x, thresh = 2^(-11/2), sample.include = NULL, diag.value = NULL, 
                 verbose = TRUE)

Arguments

x	An object to coerce to a sparse matrix. May be of class matrix, Matrix, data.frame, or data.table. When a matrix or Matrix, row and column names should be set to sample.ids; when a data.frame or data.table, should have 3 columns: ID1, ID2, and value.
thresh	Value threshold for clustering samples to make the output matrix sparse block-diagonal. When NULL, no clustering is done. See 'Details'.
sample.include	An optional vector of sample.id indicating all samples that should be included in the output matrix; see 'Details' for usage.
diag.value	When NULL (by Default), values for the diagonal of the output matrix should be provided in x. Setting diag.value to a numeric value will make all values on the diagonal of the output matrix that value.
verbose	A logical indicating whether or not to print status updates to the console; the default is TRUE.

Details

sample.include has two primary functions: 1) It can be used to subset samples provided in x. 2) sample.include can include sample.id not in x; these additional samples will be included in the output matrix, with a value of 0 for all off-diagonal elements, and the value provided by diag.value for the diagonal elements. When left NULL, the function will determine the list of samples from what is observed in x.

thresh sets a threhsold for clustering samples such that any pair with a value greater than thresh is in the same cluster. All values within a cluster are kept, even if they are below thresh. All values between clusters are set to 0, creating a sparse, block-diagonal matrix. When thresh is NULL, no clustering is done and all samples are returned in one block. This feature is useful when converting a data.frame of kinship estimates to a matrix.

Value

An object of class 'Matrix'. Samples may be in a different order than in the input x, as samples are sorted by ID or rowname within each block (including within the block of unrelateds).

Author(s)

Matthew P. Conomos

See Also

kingToMatrix and pcrelateToMatrix for functions that use this function.

UW-GAC/GENESIS documentation built on Nov. 9, 2024, 11:55 a.m.