ldByGene: Obtain LD statistics in region specified by a gene model.
In ldblock: data structures for linkage disequilibrium measures in populations

Description Usage Arguments Value Note Examples

Obtain LD statistics in region specified by a gene model.

ldByGene(
  sym = "MMP24",
  vcf = system.file("vcf/c20exch.vcf.gz", package = "ldblock"),
  flank = 1000,
  vcfSLS = "NCBI",
  genomeSLS = "hg19",
  stats = "D.prime",
  depth = 10
)

`sym`	A standard gene symbol for use with `genemodel`
`vcf`	Path to a tabix-indexed VCF file
`flank`	number of basepairs to flank gene model for search
`vcfSLS`	seqlevelsStyle (SLS) token for VCF; will be imposed on gene model
`genomeSLS`	character tag for genome, to be used with `readVcf`
`stats`	passed to `ld`
`depth`	passed to `ld`

sparse matrix representation of selected LD statistic, as returned by ld

Uses an internal function genemod4ldblock, that relies on EnsDb.Hsapiens.v75 to get gene model.

if (interactive()) {  # there is a warning owing to non-SNV present
ld1 = ldByGene(depth=150)
image(ld1[1:200,1:200], col.reg=heat.colors(120), colorkey=TRUE,
 main="SNPs in MMP24 (chr20)") 
}