GPART: Partitioning genodata based on the result obtained by using...

In sunnyeesl/BigLD: Big-LD

Partitioning genodata based on the result obtained by using Big-LD and gene region information.

Description

GPART partition the given genodata using the result obtained by Big-LD and gene region information. The algorithm partition the whole sequence into sub sequences of which size do not exceed the given threshold.

Usage

GPART(geno, SNPinfo, chrN, allgenelist, BigLDresult = NULL, minsize = 4,
  maxsize = 50)

Arguments

geno	A data frame or matrix of additive genotype data, each column is additive genotype of each SNP.
SNPinfo	A data frame or matrix of SNPs information. 1st column is rsID and 2nd column is bp position.
chrN	A integer value to specify chromosome number of the given data.
allgenelist	A data frame or matrix of Gene info data. (1st col : Genename, 2nd col : chromosome, 3rd col : start bp, 4th col : end bp)
BigLDresult	A data frame obtained by Big_LD function. If NULL(default), the GPART function first excute Big_LD function to obtain LD blocks estimation result.
minsize	A integer value specifying the lower bound of number of SNPs in a partition.
maxsize	A integer value specifying the upper bound of number of SNPs in a partition.

Author(s)

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

See Also

Big_LD

Examples

data(geno)
data(SNPinfo)
data(allgenelist)
GPART(geno, SNPinfo, 22, genelist)

sunnyeesl/BigLD documentation built on July 11, 2022, 8:01 a.m.