finemap: Finemapping of genetic regions

Description Usage Arguments Value Examples

View source: R/finemap.R

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

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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

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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 Nov. 14, 2021, 1:18 a.m.