Usage
ld_lasso_method(block.obj, block.cood = NA, Xa = NA, Y = NA, bpmap = NA,
maxcol = 5e3, p.frac = 0.10, B = 5, s2low = 5e-3, s2high = 5e1, s2.vec.length = 4, null = FALSE)
Arguments
block.obj
An object of class gwaa.data from GenABEL.
block.cood
A vector of length p+1, where p is the number of SNPs. block.cood is an indicator vector
that indicates block boundaries at all p+1 SNP bounded intervals. Use
find.bounds to create this vector.
Xa
If block.obj is NA then a genotype matrix must be provided. Xa is a
matrix of genotype values codes as 0, 1 or 2 for homozygous major,
heterozygous, or homozygous minor, respectively.
Y
If block.obj is NA then a phenotype vector Y must be provided. Y is a
vector of diagnoses, where 0 is non-diseased and 1 is diseased.
bpmap
A vector of map positions in terms of kB from the left boundary
maxcol
The upper limit on the number of
columns in the constraint matrix. This is to prevent computational
overload. Increasing maxcol may increase computation time and
memory needed.
p.frac
The fraction of SNPs allowed in LASSO model under null hypothesis. This
parameter is used in the function get.s1.
B
The number of bootstrap iterations for cp estimate.
s2low
The lower limit of the s2 vector
s2high
The upper limit of the s2 vector
s2.vec.length
The number of exponentially spaced values of s2.
null
A logical variable that indicates if analysis should be performed on
permuted phenotype vector.