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b/man/getCOCA.Rd |
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% Generated by roxygen2: do not edit by hand |
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% Please edit documentation in R/getCOCA.R |
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\name{getCOCA} |
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\alias{getCOCA} |
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\title{Get subtypes from COCA} |
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\usage{ |
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getCOCA( |
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data = NULL, |
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N.clust = NULL, |
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type = rep("gaussian", length(data)), |
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methods = "hclust", |
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distances = "euclidean" |
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) |
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} |
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\arguments{ |
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\item{data}{List of matrices.} |
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\item{N.clust}{Number of clusters.} |
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\item{type}{Data type corresponding to the list of matrics, which can be gaussian, binomial or possion.} |
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\item{methods}{A string vector storing the names of clustering methods to be used to cluster the observations in each subdataset.} |
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\item{distances}{A string vector storing the name of distances to be used in the clustering step for each subdataset.} |
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} |
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\value{ |
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A list with the following components: |
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\code{fit} an object returned by \link[coca]{coca}. |
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\code{clust.res} a data.frame storing sample ID and corresponding clusters. |
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\code{clust.dend} a dendrogram of sample clustering. |
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\code{mo.method} a string value indicating the method used for multi-omics integrative clustering. |
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} |
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\description{ |
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This function wraps the COCA (Cluster-of-Clusters Analysis) algorithm and provides standard output for `getMoHeatmap()` and `getConsensusMOIC()`. |
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} |
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\examples{ |
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# There is no example and please refer to vignette. |
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} |
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\references{ |
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Hoadley KA, Yau C, Wolf DM, et al (2014). Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell, 158(4):929-944. |
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} |