run_populations: Run STACKS Version >= 2.0 populations module

In thierrygosselin/stackr: Run stacks software pipeline for RADseq analysis inside R

Description

Run STACKS populations module inside R!

Usage

run_populations(
  P = "06_ustacks_2_gstacks",
  V = NULL,
  O = "07_populations",
  M,
  parallel.core = parallel::detectCores() - 1,
  batch.size = 10000,
  p = 1,
  r = 0.3,
  R = 0.3,
  H = TRUE,
  min.maf = NULL,
  min.mac = NULL,
  max.obs.het = NULL,
  write.single.snp = FALSE,
  write.random.snp = FALSE,
  B = NULL,
  W = NULL,
  e = NULL,
  merge.sites = FALSE,
  merge.prune.lim = NULL,
  hwe = FALSE,
  fstats = FALSE,
  fst.correction = NULL,
  p.value.cutoff = 0.05,
  k = FALSE,
  smooth.fstats = FALSE,
  smooth.popstats = FALSE,
  sigma = 150000,
  bootstrap = FALSE,
  N = 100,
  bootstrap.pifis = FALSE,
  bootstrap.fst = FALSE,
  bootstrap.div = FALSE,
  bootstrap.phist = FALSE,
  bootstrap.wl = NULL,
  ordered.export = FALSE,
  fasta.samples = TRUE,
  fasta.samples_raw = FALSE,
  fasta.loci = TRUE,
  vcf = TRUE,
  genepop = FALSE,
  structure = FALSE,
  radpainter = FALSE,
  phase = FALSE,
  fastphase = FALSE,
  plink = FALSE,
  hzar = FALSE,
  phylip = FALSE,
  phylip.var = FALSE,
  phylip.var.all = FALSE,
  treemix = FALSE,
  no.hap.exports = FALSE,
  h = FALSE,
  verbose = FALSE,
  v = FALSE,
  log.fst.comp = FALSE
)

Arguments

P	(path, character) Path to the directory containing all the STACKS files. Default: P = "06_ustacks_2_gstacks".
V	(character) Path to an input VCF file. When this module is used to filter an existing vcf file. Default: V = NULL.
O	(character) Path to a directory where to write the output files. With default: O = "07_populations", the function creates a folder inside 07_populations, with date and time appended to populations_.
M	path to a population map file. The format is a tab-separated file, with first column containing sample name and second column population id. No heather (column name). e.g. M = "02_project_info/population.map.catalog.tsv"
parallel.core	(integer) enable parallel execution with num_threads threads. Default: parallel.core = parallel::detectCores() - 1
batch.size	(integer) The number of loci (de novo mode) or chromosome (reference mode), to process in a batch. Increase to speed analysis, uses more memory, decrease to save memory). Default in de novo mode (loci/batch): batch.size = 10000. Default in reference mode (chromosome/batch): batch.size = 1.
p	(integer) Minimum number of populations a locus must be present in to process a locus. Default: p = 1.
r	(double) Minimum percentage of individuals in a population required to process a locus for that population. Default: r = 0.3.
R	(double) Minimum percentage of individuals across populations required to process a locus. Default: r = 0.3.
H	(logical) Apply the above filters haplotype wise (unshared SNPs will be pruned to reduce haplotype-wise missing data). Default: H = TRUE.
min.maf	(double) Specify a minimum minor allele frequency required to process a nucleotide site at a locus (0 < min.maf < 0.5). Default: min.maf = NULL. Recommendation: use my other R package RADIATOR to filter data based on MAF.
min.mac	(integer) Specify a minimum minor allele count required to process a nucleotide site at a locus. Default: min.mac = NULL.
max.obs.het	(double) Specify a maximum observed heterozygosity required to process a nucleotide site at a locus. Default: max.obs.het = NULL. Recommendation: use my other R package RADIATOR to filter data based on heterozygosity.
write.single.snp	(logical) Restrict data analysis to only the first SNP per locus (implies –no-haps). Default: write.single.snp = FALSE.
write.random.snp	(logical) Restrict data analysis to one random SNP per locus (implies –no-haps). Default: write.random.snp = FALSE.
B	(character) Path to a file containing Blacklisted markers to be excluded from the export. Default: B = NULL.
W	(character) Path to a file containing Whitelisted markers to include in the export. Default: W = NULL.
e	(character) Restriction enzyme name. Default: e = NULL.
merge.sites	(logical) Merge loci that were produced from the same restriction enzyme cutsite (requires reference-aligned data). Default: merge.sites = FALSE.
merge.prune.lim	(integer) When merging adjacent loci, if at least X Default: merge.prune.lim = NULL.
hwe	(logical) Calculate divergence from Hardy-Weinberg equilibrium using the exact test at the SNP level and Guo and Thompson MCMC algorithm at the haplotype level. Default: hwe = FALSE.
fstats	(logical) Enable SNP and haplotype-based F statistics. Default: fstats = FALSE.
fst.correction	(character) Specify a correction to be applied to Fst values: 'p_value', 'bonferroni_win', or 'bonferroni_gen'. Default: fst.correction = NULL.
p.value.cutoff	(double) maximum p-value to keep an Fst measurement. Also used as base for Bonferroni correction. Default: p.value.cutoff = 0.05.
k	(logical) Enable kernel-smoothed Pi, Fis, Fst, Fst', and Phi_st calculations. Default: k = FALSE.
smooth.fstats	(logical) Enable kernel-smoothed Fst, Fst', and Phi_st calculations. Default: smooth.fstats = FALSE.
smooth.popstats	(logical) Enable kernel-smoothed Pi and Fis calculations. Default: smooth.popstats = FALSE.
sigma	(integer) Standard deviation of the kernel smoothing weight distribution. Default: sigma = 150000 (150kb).
bootstrap	(logical) Turn on boostrap resampling for all smoothed statistics. Default: bootstrap = FALSE.
N	(integer) Number of bootstrap resamplings to calculate. Default: N = 100.
bootstrap.pifis	(logical) Turn on boostrap resampling for smoothed SNP-based Pi and Fis calculations. Default: bootstrap.pifis = FALSE.
bootstrap.fst	(logical) Turn on boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs. Default: bootstrap.fst = FALSE.
bootstrap.div	(logical) Turn on boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes. Default: bootstrap.div = FALSE.
bootstrap.phist	(logical) Turn on boostrap resampling for smoothed Phi_st calculations based on haplotypes. Default: bootstrap.phist = FALSE.
bootstrap.wl	(character) Path to a whitelist file. Only use bootstrap loci contained in this whitelist. Default: bootstrap.wl = NULL.
ordered.export	(logical) If data is reference aligned, exports will be ordered; only a single representative of each overlapping site. Default: ordered.export = FALSE.
fasta.samples	(logical) Output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format. stackr default is different than stacks default because I think having this info helps to identify problems. Default: fasta.samples = TRUE.
fasta.samples_raw	(logical) Output all haplotypes observed in each sample, for each locus, in FASTA format. Default: fasta.samples_raw = FALSE.
fasta.loci	(logical) Output consensus sequences of all loci, in FASTA format. stackr default is different than stacks default because I think having this info helps to identify problems. Default: fasta.loci = TRUE.
vcf	(logical) Output SNPs in Variant Call Format (VCF). Default: vcf = TRUE.
genepop	(logical) Output results in GenePop format. Default: genepop = FALSE.
structure	(logical) Output results in Structure format. Default: structure = FALSE.
radpainter	(logical) Output results results in fineRADstructure/RADpainter format. Default: radpainter = FALSE.
phase	(logical) Output genotypes in PHASE format. Default: phase = FALSE.
fastphase	(logical) Output genotypes in fastPHASE format. Default: fastphase = FALSE.
plink	(logical) Output genotypes in PLINK format. Default: plink = FALSE.
hzar	(logical) Output genotypes in Hybrid Zone Analysis using R (HZAR) format. Default: hzar = FALSE.
phylip	(logical) Output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction. Default: phylip = FALSE.
phylip.var	(logical) Include variable sites in the phylip output encoded using IUPAC notation. Default: phylip.var = FALSE.
phylip.var.all	(logical) Include all sequence as well as variable sites in the phylip output encoded using IUPAC notation. Default: phylip.var.all = FALSE.
treemix	(logical) Output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard). Default: treemix = FALSE.
no.hap.exports	(logical) Omit haplotype outputs. Default: no.hap.exports = FALSE.
h	Display this help messsage. Default: h = FALSE
verbose	turn on additional logging. Default: verbose = FALSE
v	print program version. Default: v = FALSE
log.fst.comp	(logical) Log components of Fst/Phi_st calculations to a file. Default: log.fst.comp = FALSE

Value

populations returns different output depending on arguments selected.

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.

Guo SW, Thompson EA (1992) Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics, 48, 361-372.

See Also

populations STACKS Version 2.0b

Examples

## Not run: 
pop <- stackr::run_populations(M = "population.map.tsv")

## End(Not run)

thierrygosselin/stackr documentation built on Nov. 11, 2020, 11 a.m.