subsampleDb: Subsample repertoire
In tigger: Infers Novel Immunoglobulin Alleles from Sequencing Data

subsampleDb

R Documentation

Subsample repertoire

Description

subsampleDb will sample the same number of sequences for each gene, family or allele (specified with mode) in data. Samples or subjects can be subsampled indepently by setting group.

Usage

subsampleDb(
  data,
  gene = "v_call",
  mode = c("gene", "allele", "family"),
  min_n = 1,
  max_n = NULL,
  group = NULL
)

Arguments

`data`	`data.frame` containing repertoire data.
`gene`	name of the column in `data` with allele calls. Default is `v_call`.
`mode`	one of `c("gene", "family", "allele")` defining the degree of specificity regarding allele calls when subsetting sequences. Determines how `data` will be split into subsets from which the same number of sequences will be subsampled. See also `group`.
`min_n`	minimum number of observations to sample from each groupe. A group with less observations than the minimum is excluded.
`max_n`	maximum number of observations to sample for all `mode` groups. If `NULL`, it will be set automatically to the size of the smallest group. If `max_n` is larger than the availabe number of sequences for any `mode` group, if will be automatically adjusted and the efective `max_n` used will be the size of the smallest `mode` group.
`group`	columns containing additional grouping variables, e.g. sample_id. These groups will be subsampled independently. If `max_n` is `NULL`, a `max_n` will be automatically set for each `group`.

Details

data will be split into gene, allele or family subsets (mode) from which the same number of sequences will be subsampled. If mode=gene, for each gene in the field gene from data, a maximum of max_n sequences will be subsampled. Input sequences that have multiple gene calls (ties), can be subsampled from any of their calls, but these duplicated samplings will be removed, and the final subsampled data will contain unique rows.