ldByGene {ldblock} | R Documentation

## Obtain LD statistics in region specified by a gene model.

### Description

Obtain LD statistics in region specified by a gene model.

### Usage

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

### Arguments

`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`

### Value

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

### Note

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

### Examples

    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)")
    }

[Package ldblock version 1.22.1 Index]