extract_afs_simple: Compute and store blocked allele frequency data

Description Usage Arguments Value Examples

Description

Prepare data for various ADMIXTOOLS 2 functions. Reads data from packedancestrymap or PLINK files, and computes allele frequencies for selected populations and stores it as .rds files in outdir.

Usage

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extract_afs_simple(
  pref,
  outdir,
  inds = NULL,
  pops = NULL,
  blgsize = 0.05,
  cols_per_chunk = 10,
  maxmiss = 0,
  minmaf = 0,
  maxmaf = 0.5,
  outpop = NULL,
  transitions = TRUE,
  transversions = TRUE,
  keepsnps = NULL,
  format = NULL,
  poly_only = FALSE,
  adjust_pseudohaploid = TRUE,
  verbose = TRUE
)

Arguments

pref

Prefix of PLINK/EIGENSTRAT/PACKEDANCESTRYMAP files. EIGENSTRAT/PACKEDANCESTRYMAP have to end in .geno, .snp, .ind, PLINK has to end in .bed, .bim, .fam

outdir

Directory where data will be stored.

inds

Individuals for which data should be extracted

pops

Populations for which data should be extracted. If both pops and inds are provided, they should have the same length and will be matched by position. If only pops is provided, all individuals from the .ind or .fam file in those populations will be extracted. If only inds is provided, each indivdual will be assigned to its own population of the same name. If neither pops nor inds is provided, all individuals and populations in the .ind or .fam file will be extracted.

blgsize

SNP block size in Morgan. Default is 0.05 (50 cM). If blgsize is 100 or greater, if will be interpreted as base pair distance rather than centimorgan distance.

cols_per_chunk

Number of populations per chunk. Lowering this number will lower the memory requirements when running afs_to_f2, but more chunk pairs will have to be computed.

maxmiss

Discard SNPs which are missing in a fraction of populations higher than maxmiss

minmaf

Discard SNPs with minor allele frequency less than minmaf

maxmaf

Discard SNPs with minor allele frequency greater than than maxmaf

outpop

Keep only SNPs which are heterozygous in this population

transitions

Set this to FALSE to exclude transition SNPs

transversions

Set this to FALSE to exclude transversion SNPs

keepsnps

SNP IDs of SNPs to keep. Overrides other SNP filtering options

format

Supply this if the prefix can refer to genotype data in different formats and you want to choose which one to read. Should be plink to read .bed, .bim, .fam files, or eigenstrat, or packedancestrymap to read .geno, .snp, .ind files.

adjust_pseudohaploid

Genotypes of pseudohaploid samples are usually coded as 0 or 2, even though only one allele is observed. adjust_pseudohaploid ensures that the observed allele count increases only by 1 for each pseudohaploid sample. If TRUE (default), samples that don't have any genotypes coded as 1 among the first 1000 SNPs are automatically identified as pseudohaploid. This leads to slightly more accurate estimates of f-statistics. Setting this parameter to FALSE treats all samples as diploid and is equivalent to the ADMIXTOOLS inbreed: NO option.

verbose

Print progress updates

Value

SNP metadata (invisibly)

Examples

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## Not run: 
pref = 'my/genofiles/prefix'
outdir = 'dir/for/afdata/'
extract_afs(pref, outdir)

## End(Not run)

uqrmaie1/admixtools documentation built on Sept. 16, 2020, 5:55 a.m.