XGR (version 1.1.4)

xLDsampling: Function to generate randomly sampled LD blocks

Description

xLDsampling is supposed to generate randomly sampled LD blocks. A sample block has the same boundary range as the observed, and can respect maf of the best SNP, and/or distance of the best SNP to the nearest gene. Also it can be restricted to the same chromosome. For each null LD block, it can preserve the boundary only or exactly preserve the relative SNP locations. It returns a GRL object.

Usage

xLDsampling(bLD, GR.SNP = c("dbSNP_GWAS", "dbSNP_Common",
"dbSNP_Single"),
num.samples = 2000, respect = c("maf", "distance", "both"),
restrict.chr = F, preserve = c("boundary", "exact"), seed = 825,
verbose = T, RData.location = "http://galahad.well.ox.ac.uk/bigdata")

Arguments

bLD

a bLD object, containing a set of blocks based on which to generate a null distribution

GR.SNP

the genomic regions of SNPs. By default, it is 'dbSNP_GWAS', that is, SNPs from dbSNP (version 150) restricted to GWAS SNPs and their LD SNPs (hg19). It can be 'dbSNP_Common', that is, Common SNPs from dbSNP (version 150) plus GWAS SNPs and their LD SNPs (hg19). Alternatively, the user can specify the customised GR object directly

num.samples

the number of samples randomly generated

respect

how to respect the properties of to-be-sampled LD blocks. It can be one of 'maf' (respecting the maf of the best SNP), 'distance' (respecting the distance of the best SNP to the nearest gene), and 'both' (respecting the maf and distance)

restrict.chr

logical to restrict to the same chromosome. By default, it sets to false

preserve

how to preserve the resulting null LD block. It can be one of 'boundary' (preserving the boundary of the LD block), and 'exact' (exactly preserving the relative SNP locations within the LD block). Notably, no huge difference for the boundary preserving when enrichment analysis invovles region-based genomic annotations, but it may make difference when genomic annatations are largely SNP-based (such as eQTLs)

seed

an integer specifying the seed

verbose

logical to indicate whether the messages will be displayed in the screen. By default, it sets to false for no display

RData.location

the characters to tell the location of built-in RData files. See xRDataLoader for details

Value

a GRL object, each containing an GR oject storing an instance of sampled blocks (with a meta-column 'best' for the identity, and a meta-column 'B' for the instance sequence).

See Also

xLDsampling

Examples

# NOT RUN {
# Load the XGR package and specify the location of built-in data
library(XGR)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata"

# }
# NOT RUN {
# a) provide the seed SNPs with the significance info
## load ImmunoBase
data(ImmunoBase)
## get lead SNPs reported in AS GWAS and their significance info (p-values)
gr <- ImmunoBase$AS$variant
data <- GenomicRanges::mcols(gr)[,c('Variant','Pvalue')]

# b) get LD block (EUR population)
bLD <- xLDblock(data, include.LD="EUR", LD.r2=0.8,
RData.location=RData.location)

# c) generate random samples as a GRL object
grl <- xLDsampling(bLD, GR.SNP="dbSNP_GWAS", num.samples=2000,
RData.location=RData.location)

##########################
## Advanced use: customised GR.SNP
##########################
GR.SNP <- xRDataLoader("dbSNP_GWAS", RData.location=RData.location)
grl <- xLDsampling(bLD, GR.SNP=GR.SNP, respect="both", restrict.chr=T,
preserve="exact", RData.location=RData.location)
# }