bigsnpr: snp_cor – R documentation

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snp_cor

Correlation matrix

Description

Get significant (Pearson) correlations between nearby SNPs of the same chromosome (p-values are computed using a two-sided t-test).

Usage

snp_cor(
  Gna,
  ind.row = rows_along(Gna),
  ind.col = cols_along(Gna),
  size = 500,
  alpha = 1,
  thr_r2 = 0,
  fill.diag = TRUE,
  infos.pos = NULL,
  ncores = 1
)

bed_cor(
  obj.bed,
  ind.row = rows_along(obj.bed),
  ind.col = cols_along(obj.bed),
  size = 500,
  alpha = 1,
  thr_r2 = 0,
  fill.diag = TRUE,
  infos.pos = NULL,
  ncores = 1
)

Arguments

`Gna`	A FBM.code256 (typically `<bigSNP>$genotypes`). You can have missing values in these data.
`ind.row`	An optional vector of the row indices (individuals) that are used. If not specified, all rows are used. Don't use negative indices.
`ind.col`	An optional vector of the column indices (SNPs) that are used. If not specified, all columns are used. Don't use negative indices.
`size`	For one SNP, window size around this SNP to compute correlations. Default is `500`. If not providing `infos.pos` (`NULL`, the default), this is a window in number of SNPs, otherwise it is a window in kb (genetic distance).
`alpha`	Type-I error for testing correlations. Default is `1` (no threshold is applied).
`thr_r2`	Threshold to apply on squared correlations. Default is `0`.
`fill.diag`	Whether to fill the diagonal with 1s (the default) or to keep it as 0s.
`infos.pos`	Vector of integers specifying the physical position on a chromosome (in base pairs) of each SNP. Typically `<bigSNP>$map$physical.pos`.
`ncores`	Number of cores used. Default doesn't use parallelism. You may use nb_cores.
`obj.bed`	Object of type bed, which is the mapping of some bed file. Use `obj.bed <- bed(bedfile)` to get this object.

Value

The (Pearson) correlation matrix. This is a sparse symmetric matrix.

Examples

test <- snp_attachExtdata()
G <- test$genotypes

corr <- snp_cor(G, ind.col = 1:1000)
corr[1:10, 1:10]

# Sparsity
length(corr@x) / length(corr)

bigsnpr

Analysis of Massive SNP Arrays

v1.10.8

GPL-3

Authors

Florian Privé [aut, cre], Michael Blum [ths], Hugues Aschard [ths], Bjarni Jóhann Vilhjálmsson [ths]

Initial release

2022-07-05