prio: Prioritization of inbred mouse strains for refining genetic...

Description Usage Arguments Value Examples

View source: R/prio.R

Description

This method allows to select strain combinations which best refine a specified genetic region (GRCm38). E.g. if a crossing experiment with two inbred mouse strains 'strain1' and 'strain2' resulted in a QTL, the outputted strain combinations can be used to refine the respective region in further crossing experiments.

Usage

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prio(
  chr,
  start = NULL,
  end = NULL,
  strain1 = NULL,
  strain2 = NULL,
  consequence = NULL,
  impact = NULL,
  min_strain_benef = 0.1,
  max_set_size = 3,
  return_obj = "dataframe"
)

Arguments

chr

Vector of chromosome names.

start

Optional vector of chromosomal start positions of target regions (GRCm38).

end

Optional vector of chromosomal end positions of target regions (GRCm38).

strain1

First strain set with strains from avail_strains().

strain2

Second strain set with strains from avail_strains().

consequence

Optional vector of consequence types.

impact

Optional vector of impact types.

min_strain_benef

Minimum reduction factor (min) of a single strain.

max_set_size

Maximum set of strains.

return_obj

The user can choose to get the result to be returned as data frame ("dataframe") or as a GenomicRanges::GRanges ("granges") object. Default value is "data frame".

Value

Data frame

Examples

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res = prio("chr1",
  start = 5000000, end = 6000000, strain1 = "C57BL_6J",
  strain2 = "AKR_J"
)

comment(res$genotypes)

matmu/mmus documentation built on Nov. 14, 2021, 1:18 a.m.