finemap: Finemapping of genetic regions

In matmu/mmus: In-silico methods for genetic finemapping in inbred mice

Finemapping of genetic regions

Description

Finemapping of genetic regions in 37 inbred mice by taking advantage of their very high homozygosity rate (>95 chromosomal regions (GRCm38), this method extracts homozygous SNVs for which the allele differs between two sets of strains (e.g. case vs controls) and outputs respective causal SNV/gene candidates.

Usage

finemap(
  chr,
  start = NULL,
  end = NULL,
  strain1,
  strain2,
  consequence = NULL,
  impact = NULL,
  thr1 = 0,
  thr2 = 0,
  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.
thr1	Number discordant strains in strain1. Between 0 and length(strain1)-1. 0 by default.
thr2	Number discordant strains in strain2. Between 0 and length(strain2)-1. 0 by default.
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 "dataframe".

Value

Data frame or GenomicRanges::GRanges object containing result data.

Examples

geno = finemap("chr1",
    start = 5000000, end = 6000000,
    strain1 = c("C57BL_6J"), strain2 = c(
        "129S1_SvImJ", "129S5SvEvBrd",
        "AKR_J"
    )
)

comment(geno)

matmu/mmus documentation built on Sept. 4, 2024, 9:08 p.m.