DT2RADdata: Convert a long-format data table into polyRAD's RADdata...

In j-a-thia/genomalicious: A smorgasbord of R functions for population genomic analyses

Convert a long-format data table into polyRAD's RADdata object class.

Description

Used to generate the RADdata class object from the polyRAD package described in Clark et al. (2019).

Usage

DT2RADdata(
  dat,
  chromCol = "CHROM",
  posCol = "POS",
  locusCol = "LOCUS",
  sampCol = "SAMPLE",
  refCol = "REF",
  roCol = "RO",
  altCol = "ALT",
  aoCol = "AO",
  possPloidy = list(2L),
  sampPloidy = 2L,
  contamRate = 0.001
)

Arguments

dat	Data.table: A data table of read counts for genotypes loci. Expects the columns: The chromosome (contig) ID (see param chromCol). The position information (see param posCol). The locus ID (see param locusCol). The sample ID (see param sampCol). The reference allele nucleotides (see param refCol). The reference allele read counts (see param roCol). The alternate allele nucleotides (see param altCol). The alternate allele read counts (see param aoCol). (see param freqCol)
chromCol	Character: The column name with the chromosome information. Default = 'CHROM'.
posCol	Character: The column name with the position information. Default = 'POS'.
locusCol	Character: The column name with the locus information. Default = 'LOCUS'.
sampCol	Character: The column name with the sampled individual information. Default = 'SAMPLE'. Only needed when type=='genos'.
refCol	Character: The column with the reference allele nucleotide information. Default = 'REF'.
roCol	Character: The column with the reference allele read count information. Default = 'RO'.
altCol	Character: The column with the alternate allele nucleotide information. Default = 'ALT'.
aoCol	Character: The column with the alternate allele read count information. Default = 'AO'.
possPloidy	List: A list of integers or numerics that represent the unique ploidy values in the dataset. Default is list(2), i.e., all samples have a ploidy of 2. A list of list(2, 4) would represent possible ploidies of 2 and 4.
sampPloidy	Integer/Numeric: Either a single value or a named vector of values for each sample. Default is a single value, 2, i.e., all samples have a ploidy of 2. A vector c('Ind1'=2, 'Ind2'=4, 'Ind3'=2), for example, is a vector of ploidies for three individuals, with ploidy values of 2, 4, and 2 for individuals 1, 2 and 3, respectively.
contamRate	Numeric: The contamination rate. Default is 0.001.

References

Clark et al. (2019). G3. DOI: 10.1534/g3.118.200913

Examples

library(genomalicious)
data(data_Genos)

# Using a single ploidy
RD1 <- DT2RADdata(data_Genos, sampPloidy=2)

# Using a vector of ploidies.
samps_uniq <- unique(data_Genos$SAMPLE)
samps_ploid <- rep(2, length(samps_uniq))
names(samps_ploid) <- samps_uniq

samps_ploid

RD2 <- DT2RADdata(data_Genos, sampPloidy=samps_ploid)

Specifying multiple ploidies.
samps_ploid[20:40] <- 4

samps_ploid %>% table

RD3 <- DT2RADdata(data_Genos, possPloidy=list(2, 4), sampPloidy=samps_ploid)

j-a-thia/genomalicious documentation built on Oct. 19, 2024, 7:51 p.m.