The function will transfer a numeric matrix into a matrix of colors, in which the colors represent the values of numeric matrix
● Data Source:
BioConductor
● Keywords:
● Alias: col_by_value
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A function to convert ID based on the biomaRt package.
● Data Source:
BioConductor
● Keywords:
● Alias: convertId
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The function download XML files and png files from KEGG website to local disk
● Data Source:
BioConductor
● Keywords:
● Alias: download_KEGGfile
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The function will downlaod the latest pathway gene link from KEGG website.
● Data Source:
BioConductor
● Keywords:
● Alias: download_latest_pathway
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The function will map the genes in KEGG pathway database, and then hypergegeometric tests would be used to estimate the significance of enrichment for each pathway
● Data Source:
BioConductor
● Keywords:
● Alias: find_enriched_pathway
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A function to convert ID.
● Data Source:
BioConductor
● Keywords:
● Alias: newIdMatrix
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The function parses KEGG XML (KGML) files
● Data Source:
BioConductor
● Keywords:
● Alias: parse_XMLfile
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pho_sites_count
(Package: KEGGprofile) :
number of phosphorylation sites quantified for each gene
This data set is a data.frame with number of phosphorylation sites quantified for each gene in the analysis.
● Data Source:
BioConductor
● Keywords:
● Alias: pho_sites_count
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A wrapper for function download_KEGGfile, parse_XMLfile and plot_profile
● Data Source:
BioConductor
● Keywords:
● Alias: plot_pathway
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The function will plot the correlation distributions for each enriched pathway (result from find_enriched_pathway function), and then Wilcoxon tests would be used to estimate the significance of correlations distribution between genes in each pathway and all genes.
● Data Source:
BioConductor
● Keywords:
● Alias: plot_pathway_cor
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providing 
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