bigsnpr

Long-range LD regions

LDpred2

Stacked C+T (SCT)

Class bed

Methods for the bed class

Allele frequencies

Counts

Cross-product with a vector

Product with a vector

Projecting PCA

Projecting PCA

Randomized partial SVD

Binomial(2, p) scaling

tcrossprod / GRM

Class bigSNP

bigsnpr: Analysis of Massive SNP Arrays

Liability scale

Download 1000G

Download Beagle 4.1

Download PLINK

Objects exported from other packages

Determine reference divergence

Sequence, evenly spaced on a logarithmic scale

MAF

MAX3 statistic

PRS

Estimation of ancestry proportions

Interpolate to genetic positions

Attach a "bigSNP" from backing files

Attach a "bigSNP" for examples and tests

Truncated SVD while limiting LD

Imputation

LD clumping

CODE_012: code genotype calls (3) and missing values.

Correlation matrix

Fake a "bigSNP"

Fast imputation

Fast imputation

Fixation index (Fst)

Genomic Control

Get sample information

lassosum2

LD scores

LD score regression

Independent LD blocks

Manhattan plot

Match alleles

Modify genome build

Outlier detection

Identity-by-descent

Relationship-based pruning

Quality Control

Remove samples

BGEN matrix product

Q-Q plot

Read BGEN files into a "bigSNP"

Read variant info from one BGI file

Read PLINK files into a "bigSNP"

Save modifications

Binomial(n, p) scaling

Simulate phenotypes

Split-parApply-Combine

Subset a bigSNP

Thresholding and correction

Write PLINK files from a "bigSNP"

Replace extension '.bed'