gemmaUlmmPerChr: GEMMA uLMM per chromosome

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

GEMMA uLMM per chromosome

Description

See Zhou & Stephens (Nature Genetics, 2012).

Usage

gemmaUlmmPerChr(
  y,
  X,
  snp.coords,
  recode.genos = TRUE,
  alleles = NULL,
  maf = 0.01,
  chr.ids = NULL,
  W,
  weights = NULL,
  exe = Sys.which("gemma"),
  out.dir = getwd(),
  task.id = "gemma",
  clean = "none",
  verbose = 1
)

Arguments

y	vector of phenotypes with genotype names
X	matrix of bi-allelic SNP genotypes encoded, for each SNP, in number of copies of its second allele, i.e. as allele doses in 0,1,2, with genotypes in rows and SNPs in columns; the "second" allele is arbitrary, it corresponds to the second column of alleles, which can be the minor or the major allele
snp.coords	data.frame with SNPs as row names and two columns named "coord" and "chr"
recode.genos	if TRUE, SNP genotypes in X will be recoded so that the minor allele is counted
alleles	data.frame with SNPs in rows (names as row names) and alleles in columns (exactly 2 columns are required); the second column should correspond to the allele which number of copies is counted at each SNP in X; if NULL, fake alleles will be generated
maf	SNPs with minor allele frequency strictly below this threshold will be discarded
chr.ids	set of chromosome identifiers to analyze (optional, all by default)
W	matrix of covariates with genotypes in rows (names as row names), a first column of 1 and a second column of covariates values
weights	vector of positive weights with genotype names
exe	path to the executable of GEMMA
out.dir	directory in which the data files will be found
task.id	identifier of the task (used in output file names)
clean	remove files: none, some (temporary only), all (temporary and results)
verbose	verbosity level (0/1)

Value

a data.frame with GEMMA's output for all chromosomes

Author(s)

Timothee Flutre [aut,cre], Dalel Ahmed [ctb]

See Also

link{gemma}, plotHistPval, qqplotPval

timflutre/rutilstimflutre documentation built on Aug. 18, 2024, 7:43 p.m.