ghap.slice {GHap}

Get a slice of a GHap object

Description

This function parses a binary PLINK, phased or HapGenotypes matrix and returns the slice as an R matrix.

Usage

ghap.slice(object, ids, variants, index=FALSE,
           transposed=FALSE, sparse=TRUE,
           unphase=FALSE, impute=FALSE,
           ncores=1, verbose=TRUE)

Arguments

object

A valid GHap object (phase, haplo or plink).

ids

A character or numeric vector indicating individuals to parse.

variants

A character or numeric vector indicating variants to parse. If a "GHap.haplo" object is provided, the vector must be numeric.

index

A logical value specfying if values provided for ids and variants are indices (see details).

transposed

A logical value specfying if genotypes should be transposed. If FALSE (default), the matrix is returned as variants by individuals. Otherwise, the retrieved matrix is organized as individuals by variants.

sparse

A logical value specfying if the returned matrix should be formatted as a sparse matrix (default TRUE).

unphase

A logical value specfying if phased genotypes should be retrieved as unphased allele counts. Only meaningful for "GHap.phase" objects.

impute

A logical value specfying if missing genotypes should be replaced by 0 (i.e., A0/A0 genotypes, default = FALSE). Only meaningful for "GHap.plink" objects.

ncores

A numeric value specifying the number of cores to be used in parallel computations (default = 1).

verbose

A logical value specfying whether log messages should be printed (default = TRUE).

Details

This function parses the binary input file and returns an R matrix with the requested list of variants (markers or alleles) and individuals. The argument index allows the user to specify individuals either by name (index = FALSE) or by indices as stored in the GHap object (index = TRUE). In the case of "GHap.haplo" objects, HapAlleles can only by parsed via indices.

Value

An R matrix with variants in rows and individuals in columns (this is inverted if transposed = TRUE).

Author(s)

Yuri Tani Utsunomiya <[e-mail]>

Examples

# #### DO NOT RUN IF NOT NECESSARY ###
# 
# # Copy phase data in the current working directory
# exfiles <- ghap.makefile(dataset = "example",
#                          format = "phase",
#                          verbose = TRUE)
# file.copy(from = exfiles, to = "./")
# 
# # Load data
# phase <- ghap.loadphase("example")
# 
# ### RUN ###
# 
# # Select random individuals and markers
# ind <- sample(x = unique(phase$id), size = 5)
# mkr <- sample(x = phase$marker, size = 10)
# 
# # Generate slice of the data
# ghap.slice(object = phase, ids = ind, variants = mkr)
# 
# # Import as unphased data
# ghap.slice(object = phase, ids = ind, variants = mkr,
#            unphase = TRUE)
# 
# # Return transposed matrix
# ghap.slice(object = phase, ids = ind, variants = mkr,
#            unphase = TRUE, transposed = TRUE)
# 
# # Display data as non-sparse matrix
# ghap.slice(object = phase, ids = ind, variants = mkr,
#            unphase = TRUE, transposed = TRUE,
#            sparse = FALSE)