BigLD: Estimation of LD block regions

In sunnyeesl/gpart: Human genome partitioning of dense sequencing data by identifying haplotype blocks

Description

BigLD returns the estimation of LD block regions of given data.

Usage

BigLD(geno=NULL, SNPinfo=NULL,genofile=NULL, SNPinfofile=NULL,
cutByForce=NULL, LD=c("r2", "Dprime"), CLQcut=0.5,
clstgap=40000, CLQmode=c("density", "maximal"),
leng=200, subTaskSize=1500, MAFcut=0.05, appendRare=FALSE,
hrstType=c("near-nonhrst", "fast", "nonhrst"),
hrstParam=200, chrN=NULL, startbp=-Inf, endbp=Inf)

Arguments

geno	Data frame or matrix of additive genotype data, each column is additive genotype of each SNP.
SNPinfo	Data frame or matrix of SNPs information. 1st column is rsID and 2nd column is bp position.
genofile	Character constant; Genotype data file name (supporting format: .txt, .ped, .raw, .traw, .vcf).
SNPinfofile	Character constant; SNPinfo data file name (supporting format: .txt, .map).
cutByForce	Data frame; information of SNPs which are forced to be the last SNP LD block boundary.
LD	Character constant; LD measure to use, r2 or Dprime. Default "r2".
CLQcut	Numeric constant; a threshold for the LD measure value |r|, between 0 to 1. Default 0.5.
clstgap	Numeric constant; a threshold of physical distance (bp) between two consecutive SNPs which do not belong to the same clique, i.e., if a physical distance between two consecutive SNPs in a clique greater than clstgap, then the algorithm split the cliques satisfying each clique do not contain such consecutive SNPs. Default 40000.
CLQmode	Character constant; the way to give priority among detected cliques. if CLQmode = "density" then the algorithm gives priority to the clique of largest value of (Number of SNPs)/(range of clique), else if CLQmode = "maximal", then the algorithm gives priority to the largest clique. The default is "density".
leng	Numeric constant; the number of SNPs in a preceding and a following region of each sub-region boundary, every SNP in a preceding and every SNP in a following region need to be in weak LD. Default 200.
subTaskSize	Numeric constant; upper bound of the number of SNPs in a one-take sub-region. Default 1500.
MAFcut	Numeric constant; the MAF threshold. Default 0.05.
appendRare	logical; if TRUE, the function append rare variants with MAF<MAFcut to the constructed blocks.
hrstType	Character constant; heuristic methods. If you want to do not use heuristic algorithm, set hrstType = "nonhrst". If you want to use heuristic algorithm suggested in Kim et al.,(2017), set hrstType = "fast". That algorithm is fastest heuristic algorithm and suitable when your memory capacity is not greater than 8GB. If you want to obtain the results similar to the that of non-heuristic algorithm, set hrstType = "near-nonhrst".
hrstParam	Numeric constant; parameter for heuristic algorithm "near-nonhrst". Default is 200. It is recommended that you set the parameter to greater than 150.
chrN	Numeric(or Character) constant (or vector); chromosome number to use.
startbp	Numeric constant; starting bp position of the chrN. Default -Inf.
endbp	Numeric constant; last bp position of the chrN. Default Inf.

Value

A data frame of block estimation result. Each row of data frame shows the starting SNP and end SNP of each estimated LD block.

Author(s)

Sun-Ah Kim <[e-mail]>, Yun Joo Yoo <[e-mail]>

See Also

CLQD, LDblockHeatmap

Examples

data(geno)
data(SNPinfo)
BigLD(geno=geno, SNPinfo=SNPinfo, startbp = 16058400, endbp = 16076500)

## Not run: 
BigLD(geno, SNPinfo, LD = "Dprime")
BigLD(geno, SNPinfo, CLQcut = 0.5, clstgap = 40000, leng = 200, subTaskSize = 1500)

## End(Not run)

sunnyeesl/gpart documentation built on May 9, 2019, 7:40 a.m.