Man pages for martahidalgo/hipathia
HiPathia: High-throughput Pathway Analysis

annotate_pathsAnnotates functions to pathways
brcaBRCA gene expression dataset as SummarizedExperiment
brca_dataBRCA gene expression dataset
brca_designBRCA experimental design
compWilcoxon comparison of pathways object
create_reportCreate visualization HTML
do_pcaPerforms a Principal Components Analysis
do_wilcoxonApply Wilcoxon test
exp_dataNormalized BRCA gene expression dataset
get_go_namesTranlates GO IDs to GO names
get_highest_sig_ancestorGet highest common GO ancestor of GO annotations
get_node_namesTranlates node IDs to node names
get_nodes_dataGets the object of node activation values
get_path_namesTranlates path IDs to path names
get_paths_dataGets the object of subpathway activation values
get_pathway_functionsReturns functions related to a pathway
get_pathways_annotationsGet Pathways functional annotations
get_pathways_listLists the IDs of the pathways in a pathways object
get_pathways_summaryCompute pathway summary
go_valsGene Ontology matrix of the BRCA gene expression dataset
heatmap_plotPlots subpathways heatmap
hheadHead function for SummarizedExperiment, data.frames and...
hipathiaComputes the level of activation of the subpathways for each...
igraphs_upgradeUpgrade igraphs to current version
is_accepted_speciesChecks whether a species is accepted
load_annofunsLoads annotations object
load_annotsLoads functional annotations to genes
load_entrez_hgncLoads table of translation from HGNC to Entrez
load_gobp_frameLoads GO graph information
load_gobp_netLoads GO graph
load_mgiLoads object with graph information
load_pathwaysLoads the pathways object.
load_pseudo_mgiLoads object with pseudo graph information
load_xrefLoads table of references
mgi_from_sifCreate a Pathways object from SIF files
multiple_pca_plotPlots multiple components of a PCA
node_colorGet colors of the nodes from a comparison file
node_color_per_deColors of the nodes by its differential expression
normalize_dataNormalize expression data from a SummarizedExperiment or...
normalize_pathsNormalize the pathway matrix by rows
paths_to_go_ancestorCreate path results table with highest significant GO...
path_valsPathways matrix of the BRCA gene expression dataset
pathway_comparison_plotPlots pathway with colored significant paths
pca_plotPlots two components of a PCA
quantify_termsComputes the level of activation of the functions related to...
resultsResults object
save_resultsSave results to folder
top_pathwaysComputes pathway significance
translate_dataTranslation of the rownames IDs of a SummarizedExperiment to...
translate_matrixTranslation of the rownames IDs of a matrix to Entrez IDs.
visualize_reportVisualize a HiPathia report
martahidalgo/hipathia documentation built on June 12, 2019, 8:34 a.m.