setlabel
(Package: mseapca) :
Generate binary label matrix of metabolite set
This function generates binary label matrix of metabolite IDs and metabolite sets. This is mainly used to be called by other functions, and used to count the number of metabolites in a specific metabolite set.
● Data Source:
CranContrib
● Keywords: list
● Alias: setlabel
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read_pathway
(Package: mseapca) :
Read metabolite set file (*.xml)
This function generates metabolite set list from metabolite set file (XML). This is mainly used to be called by other functions.
● Data Source:
CranContrib
● Keywords: list
● Alias: read_pathway
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pca_scaled
(Package: mseapca) :
PCA for autoscaled data
This function performs principal component analysis (PCA). In this function, data matrix is automatically scaled to zero mean and unit variance (autoscaling) for each metabolites. PC scores, factor loadings and the results of statistical test (p-value and q-value by Benjamini and Hochberg) are returned. In this function, factor loading is defined as a correlation coefficient between PC score and each metabolite levels.
● Data Source:
CranContrib
● Keywords: pca/msea
● Alias: pca_scaled
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pathway_class
(Package: mseapca) :
Convert metabolite set (multiple) / tar.gz to list
Convertion of KEGG's tar.gz files (e.g. hsa.tar.gz) to metabolite set list
● Data Source:
CranContrib
● Keywords: list
● Alias: pathway_class
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msea_sub
(Package: mseapca) :
MSEA by Subramanian et al.
This function performs metabolite set enrichment analysis implemented in the same fashion as gene set enrichment analysis (Subramanian et al. 2005). In this function, a permutation procedure is performed for a metabolite set rather than class label. This procedure corresponds to a "gene set" of permutation type in GSEA-P software (Subramanian et al. 2007). A leading-edge subset analysis is also undertaken following the standard GSEA procedure.
● Data Source:
CranContrib
● Keywords: pca/msea
● Alias: msea_sub
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msea_ora
(Package: mseapca) :
MSEA by over representation analysis
This function performs metabolite set enrichment analysis by over representation analysis (ORA). Statistical hypothesis test of cross tabulation is performed by one-sided Fisher's exact test.
● Data Source:
CranContrib
● Keywords: pca/msea
● Alias: msea_ora
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list2xml
(Package: mseapca) :
Convert metabolite set / list to XML format
This function converts metabolite set (list to XML format).
● Data Source:
CranContrib
● Keywords: list
● Alias: list2xml
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csv2list
(Package: mseapca) :
Convert metabolite set / csv to list
This function converts your own metabolite set (csv file to list).
● Data Source:
CranContrib
● Keywords: list
● Alias: csv2list
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