summary_genotypes: Summary of 'batch_x.genotypes.txt' and 'batch_x.markers.tsv'...
In thierrygosselin/stackr: Run stacks pipeline for RADseq analysis inside R

summary_genotypes

R Documentation

Summary of `batch_x.genotypes.txt` and `batch_x.markers.tsv` files.

Description

Useful summary of batch_x.genotypes.txt and batch_x.markers.tsv files produced by STACKS genotypes module use for linkage mapping. Filter segregation distortion and output JoinMap and or OneMap file.

Usage

summary_genotypes(
  genotypes,
  markers,
  filter.monomorphic = TRUE,
  filter.missing.band = TRUE,
  filter.mean.log.likelihood = NULL,
  B = NULL,
  filter.GOF = NULL,
  filter.GOF.p.value = NULL,
  ind.genotyped = 1,
  joinmap = NULL,
  onemap = NULL,
  filename = NULL
)

Arguments

`genotypes`	The `genotypes = batch_x.genotypes.txt` created by STACKS genotypes module.
`markers`	The `markers = batch_x.markers.tsv` created by STACKS genotypes module.
`filter.monomorphic`	(optional) Should monomorphic loci be filtered out. Default: `filter.monomorphic = TRUE`.
`filter.missing.band`	(optional) Should loci with missing band be filtered out. Default: `filter.missing.band = TRUE`.
`filter.mean.log.likelihood`	(optional, integer) Apply a mean log likelihood filter to the loci. e.g. filter.mean.log.likelihood = -10. Default: `filter.mean.log.likelihood = NULL` (no filter)
`B`	(optional, integer) The segregation distortion p-value will be computed with a Monte Carlo test with `B` replicates, if `B` is supplied. For more details, see `chisq.test`. Default: `B = NULL`.
`filter.GOF`	(optional, integer) Filer value of the goodness-of-fit for segregation distortion. Default: `filter.GOF = NULL`.
`filter.GOF.p.value`	(optional, double) Filer the goodness-of-fit p-value of GOF segregation distortion. Default: `filter.GOF.p.value = NULL`.
`ind.genotyped`	(optional, integer) Filter the number of individual progenies required to keep the marker. Default: `ind.genotyped = 1`.
`joinmap`	(optional) Name of the JoinMap file to write in the working directory. e.g. "joinmap.turtle.family3.loc". Default: `joinmap = NULL`.
`onemap`	(optional) Name of the OneMap file to write in the working directory. e.g. "onemap.turtle.family3.txt". Default: `onemap = NULL`.
`filename`	(optional) The name of the summary file written in the directory. No default. Default: `filename = NULL`.

Details

SIGNIFICANCE results pvalue (goodness-of-fit pvalue): <= 0.0001 = ****, <= 0.001 & > 0.0001 = ***, <= 0.01 & > 0.001 = **, <= 0.05 & > 0.01 = *.

work in progress...

Value

The function returns a list with the genotypes summary $geno.sum, joinmap markers $joinmap.sum and onemap markers $onemap.sum summary (use $ to access each components). A JoinMap and/or OneMap file can also be exported to the working direcvtory.

Author(s)

Thierry Gosselin thierrygosselin@icloud.com

References

Catchen JM, Amores A, Hohenlohe PA et al. (2011) Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences. G3, 1, 171-182.

Catchen JM, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Molecular Ecology, 22, 3124-3140.

Examples

## Not run: 
linkage.map.crab <- summary_genotypes(
genotypes = "batch_10.markers.tsv",
markers = "batch_10.genotypes_300.txt",
filter.monomorphic = TRUE,
filter.missing.band = TRUE,
filter.mean.log.likelihood = -10,
B = NULL,
ind.genotyped = 300,
joinmap = "test.loc",
onemap = "test.onemap.txt",
filename = "genotypes.summary.tsv"
)

## End(Not run)

thierrygosselin/stackr documentation built on April 13, 2025, 10:28 a.m.