bed_scaleBinom {bigsnpr} | R Documentation |
Binomial(2, p) scaling
Description
Binomial(2, p) scaling where p
is estimated.
Usage
bed_scaleBinom(
obj.bed,
ind.row = rows_along(obj.bed),
ind.col = cols_along(obj.bed),
ncores = 1
)
Arguments
obj.bed |
Object of type bed, which is the mapping of some bed file.
Use |
ind.row |
An optional vector of the row indices (individuals) that
are used. If not specified, all rows are used. |
ind.col |
An optional vector of the column indices (SNPs) that are used.
If not specified, all columns are used. |
ncores |
Number of cores used. Default doesn't use parallelism. You may use nb_cores. |
Details
You will probably not use this function as is but as parameter
fun.scaling
of other functions (e.g. bed_autoSVD
and bed_randomSVD
).
Value
A data frame with $center
and $scale
.
References
This scaling is widely used for SNP arrays. Patterson N, Price AL, Reich D (2006). Population Structure and Eigenanalysis. PLoS Genet 2(12): e190. doi:10.1371/journal.pgen.0020190.
Examples
bedfile <- system.file("extdata", "example-missing.bed", package = "bigsnpr")
obj.bed <- bed(bedfile)
str(bed_scaleBinom(obj.bed))
str(bed_randomSVD(obj.bed, bed_scaleBinom))