# Pipeline for augmented co-expression analysis

## Documentation for package ‘GWENA’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

.check_data_expr | Run checks on an object to test if it's a data_expr
.check_gost | Run checks on an object to test if it's a gost result
.check_module | Run checks on an object to test if it's a module or a list of modules
.check_network | Run checks on an object to test if it's a network
.contingencyTable | Calculate a contigency table of module overlap between datasets
.cor_func_match | Match a correlation function based on a name
associate_phenotype | Modules phenotpic association
bio_enrich | Modules enrichment
build_graph_from_sq_mat | Return graph from squared matrix network
build_net | Network building by co-expression score computation
compare_conditions | Compare modules topology between conditions
detect_modules | Modules detection in a network
filter_low_var | Filtering genes with low variability
filter_RNA_seq | Filtering of low counts
get_fit.cor | Calculating best fit of a power low on correlation matrix computed on expression data
get_fit.expr | Calculating best fit of a power low on expression data
get_hub_degree | Determine hub genes based on degree
get_hub_genes | Determine hub genes inside each module
get_hub_high_co | Determine hub genes based on connectivity
get_hub_kleinberg | Determine hub genes based on Kleinberg's score
get_sub_clusters | Detect sub clusters
gg_palette | Mimicking ggplot palette Source : https://stackoverflow.com/questions/8197559/emulate-ggplot2-default-color-palette
gtex_expr | Transcriptomic muscle data from GTEx consorsium RNA-seq data
gtex_traits | Traits data linked to samples in transcriptomic data from GTEx
is_data_expr | Determine if an object is a data_expr in sens of GWENA
is_gost | Determine if an object is a gost object
is_module | Determine if an object is a module or a list of modules
is_network | Determine if an object is a network
join_gost | Join gprofiler2::gost results
kuehne_expr | Transcriptomic data from the Kuehne et al. publication
kuehne_traits | Traits data linked to samples in transcriptomic data from the Kuehne et al. publication
plot_comparison_stats | Heatmap of comparison statistics
plot_enrichment | Plot module from bio_enrich
plot_expression_profiles | Modules expression profiles
plot_module | Plot co-expression network
plot_modules_merge | Modules merge plot
plot_modules_phenotype | Heatmap of modules phenotpic association
quiet | Muting a function
z_summary | Calculating Z summary