exportSNPPIT: write a SNPPIT input file. Will warn about skipping loci with...

In delomast/EFGLmh: Functions For Working With Microhaps for EFGL

write a SNPPIT input file. Will warn about skipping loci with > 2 alleles.

Description

write a SNPPIT input file. Will warn about skipping loci with > 2 alleles.

Usage

exportSNPPIT(
  x,
  filename,
  baseline,
  mixture,
  loci = NULL,
  errorRate = 0.005,
  POPCOLUMN_SEX = NULL,
  POPCOLUMN_REPRO_YEARS = NULL,
  POPCOLUMN_SPAWN_GROUP = NULL,
  OFFSPRINGCOLUMN_BORN_YEAR = NULL,
  OFFSRPINGCOLUMN_SAMPLE_YEAR = NULL,
  OFFSPRINGCOLUMN_AGE_AT_SAMPLING = NULL
)

Arguments

x	an EFGLdata object
filename	the name of the file to write
baseline	a vector of pops to use as the baseline (potential parents).
mixture	a vector of pops to use as the mixture (potential offspring).
loci	a vector of loci to include. If not specified, all loci are used.
errorRate	per allele error rate for all loci
POPCOLUMN_SEX	metadata column with sex info (coded as M, F, and ?)
POPCOLUMN_REPRO_YEARS	metadata column with repro years
POPCOLUMN_SPAWN_GROUP	metadata column with spawn group
OFFSPRINGCOLUMN_BORN_YEAR	metadata column with birth year
OFFSRPINGCOLUMN_SAMPLE_YEAR	metadata column with sample year
OFFSPRINGCOLUMN_AGE_AT_SAMPLING	metadata column with age at sampling

Value

nothing, just writes a file

delomast/EFGLmh documentation built on June 1, 2024, 6:55 a.m.