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Boxplot()
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Generate Boxplot using eNODAL_obj object |
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calcAtchison()
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Calculate Atchison distance of a matrix (among cols) |
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calcdist()
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Calculate different types of distance (among cols) |
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calcGower()
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Calculate Gower distance (among cols) |
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calcProp()
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Calculate proportion of each component in gam model |
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calcProp_gam()
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Calculate proportion of each component in gam model |
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calcProp_lm()
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Calculate proportion of each component in linear model |
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calctrans()
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Transformation of distance matrix |
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check_fac_num()
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Check each column of a dataframe is a factor or numerical |
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check_validity()
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check validity |
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clusterMethod()
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Run clustering method (do not need to specify number of clusters) |
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clusterMethodk()
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Run clustering method (Need to specify number of clusters) |
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ClusterPlot()
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Generate clustering result plot for eNODAL_obj object |
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createClParam()
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Create parameters list for stage II clustering. |
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createConsensus()
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Consensus clustering |
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createDistList()
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Calculate list of distance matrix |
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createDist_base()
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Run correlation distance |
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createFeatures()
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Calculate interpretable features for eNODAL object |
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createParams()
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Create parameters list for eNODAL_obj object. |
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createwD2()
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Create distance matrix with respect to the variance explained. |
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createwDist()
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Calculate weighted distance |
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cvtCooccur()
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Convert clustering result to co-occurrence matrix |
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cvt_fac_num()
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Convert a dataframe with factor and numerical to numerical with dummy code. |
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.changename()
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Change names of eNODAL_obj clustering result |
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.findConvex()
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Finding convex hull of given data |
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.hybrid_test()
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Hybrid test for eNODAL object. |
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.inhull()
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determine whether points is in convex hull |
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.nested_test()
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Nested test. |
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.npntest()
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nonparametric ANOVA test from Zhou's paper using bootstrap. |
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.unify_class()
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Unify all the type of X into matrix |
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eNODAL-class
|
eNODAL class |
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eNODAL_build()
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Build eNODAL object |
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eNODAL_example
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An example of fitted eNODAL object |
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fisher_trans()
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Fisher Transformation |
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get_clusters()
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Get clustering result of eNODAL object |
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ggSurface()
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Function to make nice surfaces using ggplot |
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hybrid_test()
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Hybrid test for eNODAL_obj object. |
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lc_stat()
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Calculate LC-Stats |
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LC_test0()
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Calculate LC-Test |
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lm_test()
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Nested test for linear model. |
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make.knn.graph()
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Make knn graph |
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NGFPlot()
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Generate NGF using eNODAL_obj object |
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Proteomics
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Part of processed mouse liver nutriomics proteomics dataset |
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runAnno()
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Add annotation for variable name |
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runeNODAL()
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Run eNODAL using with eNODAL object. |
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runHT()
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Run hypothesis testing using with eNODAL object. |
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runSubclust()
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Run subclustering using with eNODAL_obj object. |
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show_clusters()
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Print all the clustering of eNODAL result |
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trans_clr()
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Calculate centered log ratio(clr) transformation of a matrix |