Function reference • kangar00

All functions
`anno`	Example annotation file for three pathways.
`calc_kernel(<GWASdata>)` `lin_kernel(<GWASdata>)` `sia_kernel(<GWASdata>)` `net_kernel(<GWASdata>)`	Calculate the kernel-matrix for a pathway
`geno`	Example genotypes for 50 individuals.
`get_anno(<snp_info>,<pathway_info>)`	Annotates SNPs via genes to pathways
`get_network_matrix(<pathway>)`	Function to calculate the network `matrix` for a `pathway` object
`gwas`	Example `GWASdata` object.
`GWASdata()` `show(<GWASdata>)` `summary(<GWASdata>)` `GeneSNPsize(<GWASdata>)`	S4 class for an object representing a Genome-wide Assocaition Study.
`hsa04020`	Example `pathway` object for pathway hsa04020.
`hsa04022_info`	Example `pathway_info` object for `pathway` hsa04022.
`kangar00-package` `kangar00`	kangar00 package
`show(<kernel>)` `summary(<kernel>)` `plot(<kernel>,<missing>)`	An S4 class representing a kernel matrix calculated for a pathway
`show(<lkmt>)` `summary(<lkmt>)`	An S4 class to represent the variance component test.
`lkmt.net.kernel.hsa04020`	Example test result for the network-based `kernel` for `pathway` hsa04020.
`lkmt_test()` `score_test(<matrix>)` `davies_test(<matrix>)`	A function to calculate the p-values for kernel matrices.
`lowrank_kernel-class` `lowrank_kernel`	An S4 class to represent a low-rank kernel for a SNPset at specified knots
`make_psd(<matrix>)`	Adjust network `matrix` to be positive semi-definite
`net.kernel.hsa04020`	Example network-based kernel matrix for pathway hsa04020.
`pathway()` `show(<pathway>)` `summary(<pathway>)` `pathway2igraph(<pathway>)` `analyze(<pathway>)` `get_genes(<pathway>)` `plot(<pathway>,<missing>)` `sample_genes(<pathway>)`	An S4 class to represent a gene-gene interaction network
`pathway_info()` `show(<pathway_info>)` `summary(<pathway_info>)`	An S4 class for an object assigning genes to pathways
`pheno`	Example phenotype file for 50 individuals.
`read_geno(<character>)`	read genotype data from file to one of several available objects, which can be passed to a GWASdata object `GWASdata`.
`rewire_network(<pathway>)`	Rewires interactions in a `pathway`, which go through a gene not represented by any SNPs in the considered `GWASdata` dataset.
`rs10243170_info`	Example `snp_info` object for SNP rs10243170.
`snp_info()` `show(<snp_info>)` `summary(<snp_info>)`	An S4 class for an object assigning SNP positions to rs-numbers (for internal use)

Reference

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