calGeneticDist: calGeneticDist

In ruqianl/comapr: Crossover analysis and genetic map construction

calGeneticDist

Description

Calculate genetic distances of marker intervals or binned-chromosome Given whether crossover happens in each marker interval, calculate the recombination fraction in samples and then derive the Haldane or Kosambi genetic distances via mapping functions

Usage

calGeneticDist(
  co_count,
  bin_size = NULL,
  mapping_fun = "k",
  ref_genome = "mm10",
  group_by = NULL,
  chrom_info = NULL
)

## S4 method for signature 'GRanges,missing,ANY,ANY,missing'
calGeneticDist(
  co_count,
  bin_size = NULL,
  mapping_fun = "k",
  ref_genome = "mm10",
  group_by = NULL,
  chrom_info = NULL
)

## S4 method for signature 'GRanges,numeric,ANY,ANY,missing'
calGeneticDist(
  co_count,
  bin_size = NULL,
  mapping_fun = "k",
  ref_genome = "mm10",
  group_by = NULL,
  chrom_info = NULL
)

## S4 method for signature 'GRanges,missing,ANY,ANY,character'
calGeneticDist(
  co_count,
  bin_size = NULL,
  mapping_fun = "k",
  ref_genome = "mm10",
  group_by = NULL,
  chrom_info = NULL
)

## S4 method for signature 'GRanges,numeric,ANY,ANY,character'
calGeneticDist(
  co_count,
  bin_size = NULL,
  mapping_fun = "k",
  ref_genome = "mm10",
  group_by = NULL,
  chrom_info = NULL
)

## S4 method for signature 'RangedSummarizedExperiment,missing,ANY,ANY,missing'
calGeneticDist(
  co_count,
  bin_size = NULL,
  mapping_fun = "k",
  ref_genome = "mm10",
  group_by = NULL,
  chrom_info = NULL
)

## S4 method for signature 
## 'RangedSummarizedExperiment,missing,ANY,ANY,character'
calGeneticDist(
  co_count,
  bin_size = NULL,
  mapping_fun = "k",
  ref_genome = "mm10",
  group_by = NULL,
  chrom_info = NULL
)

## S4 method for signature 
## 'RangedSummarizedExperiment,numeric,ANY,ANY,character'
calGeneticDist(
  co_count,
  bin_size = NULL,
  mapping_fun = "k",
  ref_genome = "mm10",
  group_by = NULL,
  chrom_info = NULL
)

## S4 method for signature 'RangedSummarizedExperiment,numeric,ANY,ANY,missing'
calGeneticDist(
  co_count,
  bin_size = NULL,
  mapping_fun = "k",
  ref_genome = "mm10",
  group_by = NULL,
  chrom_info = NULL
)

Arguments

co_count	GRange or RangedSummarizedExperiment object, returned by countCO
bin_size	The binning size for grouping marker intervals into bins. If not supplied,the orginial marker intervals are returned with converted genetic distancens based on recombination rate
mapping_fun	The mapping function to use, can be one of "k" or "h" (kosambi or haldane)
ref_genome	The reference genome name. It is used to fetch the chromosome size information from UCSC database.
group_by,	character vector contains the unique prefix of sample names that are used for defining different sample groups. Or the column name in colData(co_count) that specify the group factor. If missing all samples are assumed to be from one group
chrom_info	A user supplied data.frame containing two columns with column names chrom and size, describing the chromosome names and lengths if not using ref_genome from UCSC. If supplied, the 'ref_genome' is ignored.

Value

GRanges object GRanges for marker intervals or binned intervals with Haldane or Kosambi centiMorgans

Examples

data(coCount)
dist_se <- calGeneticDist(coCount)
# dist_se <- calGeneticDist(coCount,group_by="sampleGroup")

ruqianl/comapr documentation built on Oct. 27, 2023, 5:12 a.m.