dense2sparse: Convert numeric genotype matrix to sparse matrix

In bravo: Bayesian Screening and Variable Selection

Convert numeric genotype matrix to sparse matrix

Description

Reads a numeric genotype file and converts it to a sparse matrix format.

Usage

dense2sparse(
  file.name,
  num.genotypes = NULL,
  separator = NULL,
  fixed = TRUE,
  recode = TRUE,
  na.strings = c("NA", ".", "-9", "NN"),
  progress = TRUE
)

Arguments

file.name	Path to the numeric genotype file. Could be (and should be) gzipped.
num.genotypes	Maximum number of genotypes to read. An upper bound is OK.
separator	"\t" or "," etc. that separates the entries in a line.
fixed	Is 'separator' a fixed string (TRUE) or a regex (FALSE)?
recode	recode each SNP so its major allele is 0 (per-SNP)
na.strings	tokens treated as missing
progress	Whether to show a progress bar (default TRUE).

Value

A sparse matrix of class dgCMatix.

bravo documentation built on June 9, 2026, 9:06 a.m.