qtl2: scan1snps – R documentation

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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,
  ...
)

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.

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)

Examples

## Not run: 
# load example data and calculate genotype probabilities
file <- paste0("https://raw.githubusercontent.com/rqtl/",
               "qtl2data/master/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)

## End(Not run)

qtl2

Quantitative Trait Locus Mapping in Experimental Crosses

v0.24

GPL-3

Authors

Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>), R Core Team [ctb]

Initial release

2020-12-16