Binomial(2, p) scaling
Binomial(2, p) scaling where p is estimated.
bed_scaleBinom( obj.bed, ind.row = rows_along(obj.bed), ind.col = cols_along(obj.bed), ncores = 1 )
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. |
You will probably not use this function as is but as parameter
fun.scaling of other functions (e.g. bed_autoSVD and bed_randomSVD).
A data frame with $center and $scale.
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.
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))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.