export_data: A function to export the data from rhapsodi

In mccoy-lab/rhapsodi: R haploid sperm/oocyte data imputation

A function to export the data from rhapsodi

Description

This function exports the data from rhapsodi by first adding index and pos columns to the gamete output data. Then, continues by checking whether the input data was originally nucleotide encoded (A/C/G/T/NA). If so, the function appends a0 and a1 columns to 0/1 encoded outputs by calling record_ref_alt, such that the nucleotide(s) associated with genotype 0 are recorded in column a0 and the nucleotide(s) associated with genotype 1 are recorded in column a1 Finally, the function returns a named list which has donor_haps which is the phased haplotypes as a data frame with column names index, pos (for SNP positions), h1 (haplotype 1), & h2 (haplotype 2) if acgt = FALSE. Otherwise: index, pos, a0, a1, h1, h2 gamete_haps which is the filled gamete data frame specifying from which donor haplotype each gamete position originates. Column names: index, pos, gamete_names. gamete_genotypes which is the filled gamete dataf rame specifying the genotype (in 0's and 1's) for each gamete position. If acgt = FALSE, column names: index, pos, gamete_names. Otherwise: index, pos, a0, a1, gamete_names unsmoothed_gamete_haps which is the filled gamete data frame specifying from which donor haplotype each gamete position originates in data frame form, after unsmoothing the data by replacing imputed values with original sequencing reads when there's disagreement between observations and imputation. Column names: index, pos, gamete_names. unsmoothed_gamete_genotypes which is the filled gamete data frame specifying the genotype (in 0's and 1's) for each gamete position, after unsmoothing the the data by replacing imputed values with original sequencing reads when there's disagreement between observations and imputation. If acgt = FALSE, column names: index, pos, gamete_names. Otherwise: index, pos, a0, a1, gamete_names recomb_breakswhich is a data frame specifying the recombination breakpoints for each gamete. Column names: Ident, Genomic_start, Genomic_end

Usage

export_data(
  input_data,
  complete_haplotypes,
  filled_gametes,
  recomb_breaks,
  acgt = FALSE
)

Arguments

input_data	the named list from read_data
complete_haplotypes	the dataframe from phase_donor_haplotypes
filled_gametes	the named list from impute_gamete_genotypes
recomb_breaks	the dataframe from discover_meitoic_recombination
acgt	a bool; default is FALSE. If TRUE, assumes that the input data was not 0/1/NA encoded, rather gamete genotypes were A/C/G/T/NA encoded and the dataframe had ref and alt columns. Will add these columns back as a0 and a1 for 0/1 encoded output data

Value

rhapsodi_out a named list with donor_haps, gamete_haps, gamete_genotypes, unsmoothed_gamete_haps, unsmoothed_gamete_genotypes, and recomb_breaks

mccoy-lab/rhapsodi documentation built on July 27, 2022, 3:56 a.m.