Man pages for jmanitz/kangar00
Kernel Approaches for Nonlinear Genetic Association Regression
| anno | Example annotation file for three pathways. |
| calc_kernel | Calculate the kernel-matrix for a pathway |
| gene_name_number-character-method | Function to get genes names and numbers from kegg (for... |
| geno | Example genotypes for 50 individuals. |
| get_ana-data.frame-method | Produce middle part of network kernel (for internal use) |
| get_anno-snp_info-pathway_info-method | Annotates SNPs via genes to pathways |
| get_network_matrix | Function to calculate the network 'matrix' for a 'pathway'... |
| gwas | Example 'GWASdata' object. |
| GWASdata-class | S4 class for an object representing a Genome-wide Assocaition... |
| hsa04020 | Example 'pathway' object for pathway hsa04020. |
| hsa04022_info | Example 'pathway_info' object for 'pathway' hsa04022. |
| kangar00-package | kangar00 package |
| kernel-class | An S4 class representing a kernel matrix calculated for a... |
| lkmt-class | An S4 class to represent the variance component test. |
| lkmt.net.kernel.hsa04020 | Example test result for the network-based 'kernel' for... |
| lkmt_test | A function to calculate the p-values for kernel matrices. |
| lowrank_kernel-class | An S4 class to represent a low-rank kernel for a SNPset at... |
| make_psd-matrix-method | Adjust network 'matrix' to be positive semi-definite |
| net.kernel.hsa04020 | Example network-based kernel matrix for pathway hsa04020. |
| pathway-class | An S4 class to represent a gene-gene interaction network |
| pathway_info-class | An S4 class for an object assigning genes to pathways |
| pheno | Example phenotype file for 50 individuals. |
| read_geno-character-method | read genotype data from file to one of several available... |
| rewire_network | Rewires interactions in a 'pathway', which go through a gene... |
| rs10243170_info | Example 'snp_info' object for SNP rs10243170. |
| set_names-matrix-method | Helper function to translate gene numbers to names |
| set_one-matrix-method | Helper function to set 'matrix' entries to 0/1/-1 only |
| snp_info-class | An S4 class for an object assigning SNP positions to... |
