gemmaUlmmPerChr | R Documentation |
See Zhou & Stephens (Nature Genetics, 2012).
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
)
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 |
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 |
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) |
a data.frame with GEMMA's output for all chromosomes
Timothee Flutre [aut,cre], Dalel Ahmed [ctb]
link{gemma}
, plotHistPval
, qqplotPval
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