bigsnpr-package: bigsnpr: Analysis of Massive SNP Arrays

In bigsnpr: Analysis of Massive SNP Arrays

bigsnpr: Analysis of Massive SNP Arrays

Description

Easy-to-use, efficient, flexible and scalable tools for analyzing massive SNP arrays. Privé et al. (2018) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/bioinformatics/bty185")}.

Arguments

G	A FBM.code256 (typically ⁠<bigSNP>$genotypes⁠). You shouldn't have missing values. Also, remember to do quality control, e.g. some algorithms in this package won't work if you use SNPs with 0 MAF.
Gna	A FBM.code256 (typically ⁠<bigSNP>$genotypes⁠). You can have missing values in these data.
x	A bigSNP.
infos.chr	Vector of integers specifying each SNP's chromosome. Typically ⁠<bigSNP>$map$chromosome⁠.
infos.pos	Vector of integers specifying the physical position on a chromosome (in base pairs) of each SNP. Typically ⁠<bigSNP>$map$physical.pos⁠.
nploidy	Number of trials, parameter of the binomial distribution. Default is 2, which corresponds to diploidy, such as for the human genome.
ind.row	An optional vector of the row indices (individuals) that are used. If not specified, all rows are used. Don't use negative indices.
ind.col	An optional vector of the column indices (SNPs) that are used. If not specified, all columns are used. Don't use negative indices.
ncores	Number of cores used. Default doesn't use parallelism. You may use bigstatsr::nb_cores().
is.size.in.bp	Deprecated.
obj.bed	Object of type bed, which is the mapping of some bed file. Use obj.bed <- bed(bedfile) to get this object.

Author(s)

Maintainer: Florian Privé [e-mail]

Other contributors:

• Michael Blum [thesis advisor]

• Hugues Aschard [e-mail] [thesis advisor]

• Bjarni Jóhann Vilhjálmsson [e-mail] [thesis advisor]

See Also

Useful links:

• https://privefl.github.io/bigsnpr/

• Report bugs at https://github.com/privefl/bigsnpr/issues

bigsnpr documentation built on Sept. 30, 2024, 9:18 a.m.