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