tidypopgen (version 0.4.3)

gen_tibble: Constructor for a gen_tibble

Description

A gen_tibble stores genotypes for individuals in a tidy format. DESCRIBE here the format

Usage

gen_tibble(
  x,
  ...,
  valid_alleles = c("A", "T", "C", "G"),
  missing_alleles = c("0", "."),
  backingfile = NULL,
  allow_duplicates = FALSE,
  quiet = FALSE
)
# S3 method for character
gen_tibble(
  x,
  ...,
  parser = c("cpp", "vcfR"),
  n_cores = 1,
  chunk_size = NULL,
  valid_alleles = c("A", "T", "C", "G"),
  missing_alleles = c("0", "."),
  backingfile = NULL,
  allow_duplicates = FALSE,
  quiet = FALSE
)
# S3 method for matrix
gen_tibble(
  x,
  indiv_meta,
  loci,
  ...,
  ploidy = 2,
  valid_alleles = c("A", "T", "C", "G"),
  missing_alleles = c("0", "."),
  backingfile = NULL,
  allow_duplicates = FALSE,
  quiet = FALSE
)

Value

an object of the class gen_tbl.

Arguments

x

can be:

• a string giving the path to a PLINK BED or PED file. The associated BIM and FAM files for the BED, or MAP for PED are expected to be in the same directory and have the same file name.

• a string giving the path to a RDS file storing a bigSNP object from the bigsnpr package (usually created with bigsnpr::snp_readBed())

• a string giving the path to a vcf file. Only biallelic SNPs will be considered.

• a string giving the path to a packedancestry .geno file. The associated .ind and .snp files are expected to be in the same directory and share the same file name prefix.

• a genotype matrix of dosages (0, 1, 2, NA) giving the dosage of the alternate allele.

...

if x is the name of a vcf file, additional arguments passed to vcfR::read.vcfR(). Otherwise, unused.

valid_alleles

a vector of valid allele values; it defaults to 'A','T', 'C' and 'G'.

missing_alleles

a vector of values in the BIM file/loci dataframe that indicate a missing value for the allele value (e.g. when we have a monomorphic locus with only one allele). It defaults to '0' and '.' (the same as PLINK 1.9).

backingfile

the path, including the file name without extension, for backing files used to store the data (they will be given a .bk and .RDS automatically). This is not needed if x is already an .RDS file. If x is a .BED or a VCF file and backingfile is left NULL, the backing file will be saved in the same directory as the bed or vcf file, using the same file name but with a different file type (.bk rather than .bed or .vcf). If x is a genotype matrix and backingfile is NULL, then a temporary file will be created (but note that R will delete it at the end of the session!)

allow_duplicates

logical. If TRUE, the tibble will allow duplicated loci (those with genomic coordinate (chromosome + position) or locus name appearing more than once). If FALSE, an error will be thrown if duplicated loci are found. These validations run before backing files are saved. Default is FALSE.

quiet

provide information on the files used to store the data

parser

the name of the parser used for VCF, either "cpp" to use a fast C++ parser (the default), or "vcfR" to use the R package vcfR. The latter is slower but more robust; if "cpp" gives an error, try using "vcfR" in case your VCF has an unusual structure.

n_cores

the number of cores to use for parallel processing

chunk_size

the number of loci or individuals (depending on the format) processed at a time (currently used if x is a vcf with parser "vcfR")

indiv_meta

a list, data.frame or tibble with compulsory columns 'id' and 'population', plus any additional metadata of interest. This is only used if x is a genotype matrix. Otherwise this information is extracted directly from the files.

loci

a data.frame or tibble, with compulsory columns 'name', 'chromosome', and 'position','genetic_dist', 'allele_ref' and 'allele_alt'. This is only used if x is a genotype matrix. Otherwise this information is extracted directly from the files.

ploidy

the ploidy of the samples (either a single value, or a vector of values for mixed ploidy). Only used if creating a gen_tibble from a matrix of data; otherwise, ploidy is determined automatically from the data as they are read.

Details

• VCF files: the fast cpp parser is used by default. Both cpp and vcfR parsers attempt to establish ploidy from the first variant; if that variant is found in a sex chromosome (or mtDNA), the parser will fail with 'Error: a genotype has more than max_ploidy alleles...'. To successful import such a VCF, change the order of variants so that the first chromosome is an autosome using a tool such as vcftools. Currently, only biallelic SNPs are supported. If haploid variants (e.g. sex chromosomes) are included in the VCF, they are not transformed into homozygous calls. Instead, reference alleles will be coded as 0 and alternative alleles will be coded as 1.

• packedancestry files: When loading packedancestry files, missing alleles will be converted from 'X' to NA

Examples

# \dontshow{
data.table::setDTthreads(2)
RhpcBLASctl::blas_set_num_threads(2)
RhpcBLASctl::omp_set_num_threads(2)
# }
# Create a gen_tibble from a .bed file
bed_file <-
  system.file("extdata", "lobster", "lobster.bed", package = "tidypopgen")
gen_tibble(bed_file,
  backingfile = tempfile("lobsters"),
  quiet = TRUE
)

# Create a gen_tibble from a .vcf file
vcf_path <-
  system.file("extdata", "anolis",
    "punctatus_t70_s10_n46_filtered.recode.vcf.gz",
    package = "tidypopgen"
  )
gen_tibble(vcf_path, quiet = TRUE, backingfile = tempfile("anolis_"))

# Create a gen_tibble from a matrix of genotypes:
test_indiv_meta <- data.frame(
  id = c("a", "b", "c"),
  population = c("pop1", "pop1", "pop2")
)
test_genotypes <- rbind(
  c(1, 1, 0, 1, 1, 0),
  c(2, 1, 0, 0, 0, 0),
  c(2, 2, 0, 0, 1, 1)
)
test_loci <- data.frame(
  name = paste0("rs", 1:6),
  chromosome = paste0("chr", c(1, 1, 1, 1, 2, 2)),
  position = as.integer(c(3, 5, 65, 343, 23, 456)),
  genetic_dist = as.double(rep(0, 6)),
  allele_ref = c("A", "T", "C", "G", "C", "T"),
  allele_alt = c("T", "C", NA, "C", "G", "A")
)

gen_tibble(
  x = test_genotypes,
  loci = test_loci,
  indiv_meta = test_indiv_meta,
  valid_alleles = c("A", "T", "C", "G"),
  quiet = TRUE
)