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

In MouseFM: In-silico methods for genetic finemapping in inbred mice

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

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

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

comment(res$genotypes)

MouseFM documentation built on Nov. 8, 2020, 7:26 p.m.