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
      = "gQTLstats"), flank = 1000, vcfSLS = "NCBI", genomeSLS = "hg19",
      stats = "D.prime", depth = 10)

### Arguments

`sym` | A standard gene symbol
`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. Default VCF comes from gQTLstats

### Examples

    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 1.14.3 Index]