subset.haplohh: Subsets object of 'haplohh-class'

In rehh: Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests

Description

Subsets the data of an object of class haplohh-class, meeting certain conditions.

Usage

## S3 method for class 'haplohh'
subset(
  x,
  select.hap = NULL,
  select.mrk = NULL,
  min_perc_geno.hap = NA,
  min_perc_geno.mrk = 100,
  min_maf = NA,
  max_alleles = NA,
  verbose = TRUE,
  ...
)

Arguments

x	object of class haplohh-class to be subset.
select.hap	expression, indicating haplotypes to select.
select.mrk	expression, indicating markers to select.
min_perc_geno.hap	threshold on percentage of missing data for haplotypes (haplotypes with less than min_perc_geno.hap percent of markers genotyped are discarded). Default is NA, hence no constraint.
min_perc_geno.mrk	threshold on percentage of missing data for markers (markers genotyped on less than min_perc_geno.mrk percent of haplotypes are discarded). By default, min_perc_geno.mrk=100, hence only fully genotyped markers are retained. This value cannot be set to NA or zero.
min_maf	threshold on the Minor Allele Frequency. Markers having a MAF lower than or equal to minmaf are discarded. In case of multi-allelic markers the second-most frequent allele is referred to as minor allele. Setting this value to zero eliminates monomorphic sites. Default is NA, hence no constraint.
max_alleles	threshold for the maximum number of different alleles at a site. Default is NA, hence no restriction. In order to retain only bi-allelic markers, set this parameter to 2.
verbose	logical. If TRUE (default), report verbose progress.
...	further arguments are ignored.

See Also

haplohh-class, data2haplohh

Examples

#example haplohh object (280 haplotypes, 1424 SNPs)
#see ?haplohh_cgu_bta12 for details
data(haplohh_cgu_bta12)
#select subset of first 10 hyplotypes and first 5 markers
subset(haplohh_cgu_bta12, select.hap = 1:10, select.mrk = 1:5)

rehh documentation built on Sept. 15, 2021, 5:06 p.m.