JAM_RankCheck: JAM rank check.

In pjnewcombe/R2BGLiMS: R interface to the java package BGLiMS (Bayesian Generalised Linear Model Selection).

Description

Checks the rank of a reference genotype matrix, which is required to run JAM.

Usage

JAM_RankCheck(X.ref = NULL)

Arguments

X.ref

Reference genotype matrix used by JAM to impute the SNP-SNP correlations. If multiple regions are to be analysed this should be a list containing reference genotype matrices for each region. Individual's genotype must be coded as a numeric risk allele count 0/1/2. Non-integer values reflecting imputation may be given. NB: The risk allele coding MUST correspond to that used in marginal.betas. These matrices must each be positive definite and the column names must correspond to the names of the marginal.betas vector.

Value

TRUE/FALSE of whether the matrix is full rank (hopefully it is and TRUE is returned). If X.ref is a list of reference matrices for different regions, a vector of boolen TRUE/FALSE values is returned, one for each LD block.

Author(s)

Paul Newcombe

See Also

See also JAM.

pjnewcombe/R2BGLiMS documentation built on Feb. 10, 2020, 8:52 p.m.