ldByGene {ldblock} | R Documentation |
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 |
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
|
stats |
passed to |
depth |
passed to |
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)") }