mPhen.simulate
(Package: MultiPhen) :
Simulates phenotypes according to a correlation structure.
This function simulates phenotypes based on a pre-defined correlation structure (which can also be obtained from mPhen.sampleCovar), and a genetic effect x. The function works by sampling a phenotype from a correlation matrix in a linearly transformed space such that the genetic effect direction is only in the direction of the x-axis, then transforming back into the original space. If inverse is TRUE, then the phenotypes are sampled first with no genetic effect, then the genotype is sampled according to the effect direction.
This command is used to get options which can be modified to control the behaviour of MultiPhen commands. It provides a list of options which are relevant to a particular command. For example, mPhen.assoc() has its behavioiur controlled by options in mPhen.options("regression"). In order to get a list of all options, you can type mPhen.options(descr=TRUE).
Plots the corrleation between phenotype values, with different genotypes coloured differently. Note that this will plot (dim(pheno_to_plot)[2] -1 )* dim(geno)[2] plots
This function can be use to sample covariance matrices. This is useful when simulating data to test Multiphenotype based association strategies. This function lets the user decide on the orthoganality within 'blocks' and between 'blocks' of correlated variables/
This function is called by mPhen. If you are doing association on multiple batches of genotype data, it is more efficient to use this function, and to pre-prepare a 'phenoObject' object once and then use this function
Opens a read connection to a list of files which have a VCF-like format. Can read a .gz file. Also supports plink bed format. Also supports cnvPipe format. Also supports a .zip file format used by cnvHap.
providing 
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