bdget_maf_hdf5: Get minor allele frequency

In BigDataStatMeth: Statistical Methods and Algorithms for Big Data

Get minor allele frequency

Description

This function normalize data scaling, centering or scaling and centering in a dataset stored in hdf5 file

Usage

bdget_maf_hdf5(
  filename,
  group,
  dataset,
  byrows = NULL,
  bparallel = NULL,
  wsize = NULL
)

Arguments

filename	string file name where dataset to normalize is stored
group	string Matrix
dataset	string Matrix
byrows,	boolean, default TRUE. If true, the frequency is calculated by rows, else, if byrows= FALSE, frequency is calculated by columns
bparallel,	boolean, Perform calculous in parallel?, by default TRUE.
wsize	integer (default = 1000), file block size to read to perform normalization

Value

Numeric vector with allele frequencies

Examples

library(BigDataStatMeth)

maf_cols = resc <- bdget_maf_hdf5("/Users/mailos/tmp/test/test.hdf5", 
                                          "test", "mat1", byrows = FALSE )
maf_rows = resc <- bdget_maf_hdf5("/Users/mailos/tmp/test/test.hdf5", 
                                          "test", "mat1", byrows = TRUE )

BigDataStatMeth documentation built on March 30, 2022, 1:07 a.m.