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 = "gQTLstats"), 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
if (.Platform$OS.type == "unix") { ld1 = ldByGene(depth=150) image(ld1[1:200,1:200], col.reg=heat.colors(120), colorkey=TRUE, main="SNPs in MMP24 (chr20)") }