rehh (version 3.1.2)

subset.haplohh: Subsets object of haplohh-class

Description

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

Usage

# S3 method for haplohh
subset(
  x,
  select.hap = NULL,
  select.mrk = NULL,
  min_perc_geno.hap = NA,
  min_perc_geno.mrk = 100,
  min_maf = 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.

verbose

logical. If TRUE (default), report verbose progress.

...

further arguments are ignored.

See Also

haplohh-class, data2haplohh

Examples

# NOT RUN {
#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)
# }