Function reference • meNet

Functions
Network Functions Functions for reconstruction, community detection and plotting of methylation multiplex.
`meNet_cor()`	CpG network: edges based on correlation
`meNet_singleCGI()`	CpG network for a single CpG island
`meNet_CGI()`	CpG network: edges are based on CpG island affiliation
`meNet_singleGene()`	CpG network for a single gene
`meNet_gene()`	CpG network: edges are based on gene affiliation
`meMultiplex()`	Multiplex: `meNet` file from two `igraph` layers
`meMultiplex_communities()`	Multiplex community structure
`meMultiplex_to_multinet()`	Multiplex: `meNet` file to `multinet` object
`plot_multiplex()`	Multiplex plot
Resampling Functions Functions which estimate the variability of correlation and calculte p-value of the correlation permutation test.
`cor_resamplingStats()`	Mean and standard deviation of correlation
`cor_permutationTest()`	Correlation permutation test
Methylation Plot Functions Beta value error plots which use CpG coordinates to position them on x-axis.
`plotCI_meCpG()`	Beta value error plot with CpG coordinates
`plotCI_meCGI()`	Beta value error plot for a CpG island
Other Functions Secondary functions mostly called from the main functions.
`boxed_heatmap()`	Heat map without the use of `layout` function
`CpG_in_CGI()`	CpGs within a CpG island
`find_CpG()`	CpG coordinates on a chromosome
`read_infomap_communities()`	Multiplex community structure from file
`coord_sort()`	Sorting CpGs by coordinate
`max_normalization()`	Maximum normalization
`neg_max_normalization()`	Negative maximum normalization
Data
Description Tables Data frames that contain information about methylation and genomic data.
`CpG_annoHM450K`	Description of HM450K CpG sites
`CpG_genes`	Genes associated with HM450K CpG sites
`UCSC_CGI`	UCSC CpG islands
`UCSC_genes`	UCSC transcripts
`N_ranges`	Unsequences genome
Methylation Data Examples of methylation data set to be used to test the functionalities of the package.
`Bacalini_betaValues`	Bacalini HM450K methylation data
`Bacalini_sampleSheet`	Bacalini sample sheet
`Johansson_residuals`	Johansson HM450K methylation data

Reference

Functions

Network Functions

Resampling Functions

Methylation Plot Functions

Other Functions

Data

Description Tables

Methylation Data