bdremove_maf_hdf5: Remove SNPs in hdf5 omic dataset with low data

In BigDataStatMeth: Statistical Methods and Algorithms for Big Data

Remove SNPs in hdf5 omic dataset with low data

Description

Remove SNPs in hdf5 omic dataset with low data

Usage

bdremove_maf_hdf5(
  filename,
  group,
  dataset,
  outgroup,
  outdataset,
  maf,
  bycols,
  blocksize
)

Arguments

filename,	character array indicating the name of the file to create
group,	character array indicating the input group where the data set to be imputed is.
dataset,	character array indicating the input dataset to be imputed
outgroup,	character array indicating group where the data set will be saved after remove data with if 'outgroup' is NULL, output dataset is stored in the same input group.
outdataset,	character array indicating dataset to store the resulting data after imputation if 'outdataset' is NULL, input dataset will be overwritten.
maf,	by default maf = 0.05. Numeric indicating the percentage to be considered to remove SNPs, SNPS with higest MAF will be removed from data
bycols,	boolean by default = true, if true, indicates that SNPs are in cols, if SNPincols = false indicates that SNPs are in rows.
blocksize,	integer, block size dataset to read/write and calculate MAF, by default this operations is made in with 100 rows if byrows = true or 100 cols if byrows = false.

Value

Original hdf5 data file with imputed data

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