create_probs_query_func: Create a function to query genotype probabilities

In byandell/qtl2pattern: Pattern Support for 'qtl2' Package

Create a function to query genotype probabilities

Description

Create a function that will connect to a database of genotype probability information and return a list with 'probs' object and a 'map' object.

Usage

create_probs_query_func(dbfile, method_val = "fst", probdir_val = "genoprob")

Arguments

dbfile	Name of database file
method_val	either "fst" or "calc" for type of genotype probabilities
probdir_val	name of probability directory (default "genoprob")

Details

Note that this function assumes that probdir_val has a file with the physical map with positions in Mbp and other files with genotype probabilities. See read_probs for details on how probabilities are read. See create_variant_query_func for original idea.

Value

Function with six arguments, 'chr', 'start', 'end', 'allele', 'method' and 'probdir'. It returns a list with 'probs' and 'map' objects spanning the region specified by the first three arguments. The 'probs' element should be either a 'calc_genoprob' or 'fst_genoprob' object (see fst_genoprob).

Examples

dirpath <- "https://raw.githubusercontent.com/rqtl/qtl2data/master/DOex"

create_qv <- function(dirpath) {
  # Download SNP info for DOex from web via RDS.
  # snpinfo is referenced internally in the created function.
  
  tmpfile <- tempfile()
  download.file(file.path(dirpath, "c2_snpinfo.rds"), tmpfile, quiet=TRUE)
  snpinfo <- readRDS(tmpfile)
  unlink(tmpfile)
  snpinfo <- dplyr::rename(snpinfo, pos = pos_Mbp)
  
  function(chr, start, end) {
    if(chr != "2") return(NULL)
    if(start < 96.5) start <- 96.5
    if(end > 98.5) end <- 98.5
    if(start >= end) return(NULL)
    dplyr::filter(snpinfo, .data$pos >= start, .data$pos <= end)
  }
}

query_variants <- create_qv(dirpath)


create_qg <- function(dirpath) {
  # Download Gene info for DOex from web via RDS
  # gene_tbl is referenced internally in the created function.
  
  tmpfile <- tempfile()
  download.file(file.path(dirpath, "c2_genes.rds"), tmpfile, quiet=TRUE)
  gene_tbl <- readRDS(tmpfile)
  unlink(tmpfile)
  
  function(chr, start, end) {
    if(chr != "2") return(NULL)
    if(start < 96.5) start <- 96.5
    if(end > 98.5) end <- 98.5
    if(start >= end) return(NULL)
    dplyr::filter(gene_tbl, .data$end >= start, .data$start <= end)
  }
}

query_genes <- create_qg(dirpath)


# Examples for probs require either FST or RDS storage of data.

byandell/qtl2pattern documentation built on Nov. 9, 2023, 7:57 p.m.