scan1snps: Single-QTL genome scan at imputed SNPs

Description

Perform a single-QTL scan across the genome or a defined region at SNPs genotyped in the founders, by Haley-Knott regression or a liear mixed model, with possible allowance for covariates.

Usage

scan1snps(
  genoprobs,
  map,
  pheno,
  kinship = NULL,
  addcovar = NULL,
  Xcovar = NULL,
  intcovar = NULL,
  weights = NULL,
  reml = TRUE,
  model = c("normal", "binary"),
  query_func = NULL,
  chr = NULL,
  start = NULL,
  end = NULL,
  snpinfo = NULL,
  batch_length = 20,
  keep_all_snps = FALSE,
  cores = 1,
  ...
)

Value

A list with two components: lod (matrix of LOD scores) and snpinfo (a data frame of SNPs that were scanned, including columns index which indicates groups of equivalent SNPs)

Arguments

genoprobs

Genotype probabilities as calculated by calc_genoprob().

map

Physical map for the positions in the genoprobs object: A list of numeric vectors; each vector gives marker positions for a single chromosome.

pheno

A numeric matrix of phenotypes, individuals x phenotypes.

kinship

Optional kinship matrix, or a list of kinship matrices (one per chromosome), in order to use the LOCO (leave one chromosome out) method.

addcovar

An optional numeric matrix of additive covariates.

Xcovar

An optional numeric matrix with additional additive covariates used for null hypothesis when scanning the X chromosome.

intcovar

An optional numeric matrix of interactive covariates.

weights

An optional numeric vector of positive weights for the individuals. As with the other inputs, it must have names for individual identifiers.

reml

If kinship provided: if reml=TRUE, use REML; otherwise maximum likelihood.

model

Indicates whether to use a normal model (least squares) or binary model (logistic regression) for the phenotype. If model="binary", the phenotypes must have values in \([0, 1]\).

query_func

Function for querying SNP information; see create_variant_query_func()). Takes arguments chr, start, end, (with start and end in the units in map, generally Mbp), and returns a data frame containing the columns snp, chr, pos, and sdp. (See snpinfo below.)

chr

Chromosome or chromosomes to scan

start

Position defining the start of an interval to scan. Should be a single number, and if provided, chr should also have length 1.

end

Position defining the end of an interval to scan. Should be a single number, and if provided, chr should also have length 1.

snpinfo

Optional data frame of SNPs to scan; if provided, query_func, chr, start, and end are ignored. Should contain the following columns:

chr - Character string or factor with chromosome
pos - Position (in same units as in the "map").
sdp - Strain distribution pattern: an integer, between 1 and \(2^n - 2\) where \(n\) is the number of strains, whose binary encoding indicates the founder genotypes
snp - Character string with SNP identifier (if missing, the rownames are used).

batch_length

Interval length (in units of map, generally Mbp) to scan at one time.

keep_all_snps

SNPs are grouped into equivalence classes based on position and founder genotypes; if keep_all_snps=FALSE, the return value will contain information only on the indexed SNPs (one per equivalence class).

cores

Number of CPU cores to use, for parallel calculations. (If 0, use parallel::detectCores().) Alternatively, this can be links to a set of cluster sockets, as produced by parallel::makeCluster().

...

Additional control parameters passed to scan1()

Details

The analysis proceeds as follows:

Call query_func() to grab all SNPs over a region.
Use index_snps() to group SNPs into equivalence classes.
Use genoprob_to_snpprob() to convert genoprobs to SNP probabilities.
Use scan1() to do a single-QTL scan at the SNPs.

Examples

Run this code

if (FALSE) {
# load example data and calculate genotype probabilities
file <- paste0("https://raw.githubusercontent.com/rqtl/",
               "qtl2data/main/DOex/DOex.zip")
DOex <- read_cross2(file)
probs <- calc_genoprob(DOex, error_prob=0.002)

snpdb_file <- system.file("extdata", "cc_variants_small.sqlite", package="qtl2")
queryf <- create_variant_query_func(snpdb_file)

out <- scan1snps(probs, DOex$pmap, DOex$pheno, query_func=queryf, chr=2, start=97, end=98)
}