imputed.snp.scan.h2lmm: Run a SNP-based genome scan from probabilities stored in a...

In gkeele/miqtl: Suite of QTL Mapping Functions

Run a SNP-based genome scan from probabilities stored in a genome cache directory and founder strain alleles stored .allele files

Description

This function primarily takes a formula, data frame, genome cache, and directory of founder strain .alleles files to run a genome scan.

Usage

imputed.snp.scan.h2lmm(
  data,
  formula,
  K,
  allele.dir = NULL,
  genomecache,
  model = c("additive", "full"),
  use.par = "h2",
  chr = "all",
  brute = TRUE,
  use.fix.par = FALSE,
  just.these.loci = NULL,
  print.locus.fit = FALSE,
  use.progress.bar = TRUE,
  condition.loci = NULL,
  exclusion.freq = .Machine$double.eps,
  X.list = NULL,
  return.X.list = FALSE,
  ...
)

Arguments

data	A data frame with outcome and potential covariates. Should also have individual IDs that link to IDs in the genome cache with a column named "SUBJECT.NAME".
formula	An lm style formula with functions of outcome and covariates contained in data frame.
K	DEFAULT: NULL. A positive semi-definite relationship matrix, usually a realized genetic relationship matrix (GRM) based on SNP genotypes or the founder haplotype probabilities. Colnames and rownames should match the SUBJECT.NAME column in the data frame. If no K matrix is specified, either lmer is used (if sparse random effects are included in the formula) or a fixed effect model (equivalent to lm).
allele.dir	DEFAULT: NULL. The path to the directory of .allele files that specify which SNP alleles correspond to which founder haplotype. If NULL, X.list must be provided.
genomecache	The path to the genome cache directory. The genome cache is a particularly structured directory that stores the haplotype probabilities/dosages at each locus. It has an additive model subdirectory and a full model subdirectory. Each contains subdirectories for each chromosome, which then store .RData files for the probabilities/dosages of each locus.
model	DEFAULT: additive. Specifies how to model the founder haplotype probabilities. The additive options specifies use of SNP dosages, and is most commonly used. The full option regresses the phenotype on the actual genotype probabilities.
chr	DEFAULT: "all". Specifies which chromosomes to scan.
brute	DEFAULT: TRUE. During the optimization to find maximum likelihood parameters, this specifies checking the boundaries of h2=0 and h2=1. Slightly less efficient, but otherwise the optimization procedure will not directly check these values.
use.fix.par	DEFAULT: TRUE. This specifies an approximate fitting of mixed effect model (Kang et al. 2009). Much more efficient, as the optimization of h2 only needs to be performed once for the null model rather than every locus. Technically less powerful, though in practice it has proven to be almost equal to the exact procedure.
just.these.loci	DEFAULT: NULL. Specifies a reduced set of loci to fit.
print.locus.fit	DEFAULT: FALSE. If TRUE, prints out how many loci have been fit currently.
use.progress.bar	DEFAULT: TRUE. If TRUE, a progress bar is used.
exclusion.freq	DEFAULT: .Machine$double.eps. Loci with observed minor allele frequencies beneath the specified value are removed from the scan.
X.list	DEFAULT: NULL. This specifies the SNP-based design matrices for all the loci. If a scan of the same population with the same markers has been performed, this option can save a lot of time.
return.X.list	DEFAULT: FALSE. The scan procedure can return the list of design matrices for all loci. It does increase the size of the output, though can then be used as an input for subsequent scans of the same data.

Examples

imputed.snp.scan.h2lmm()

gkeele/miqtl documentation built on June 13, 2022, 4:20 p.m.