buildAvgLoading {GenomicSuperSignature} | R Documentation

## Calculate average loadings of each cluster

### Description

Calculate average loadings of each cluster

### Usage

    buildAvgLoading(dat, k, n = 20, cluster = NULL, study = TRUE)

### Arguments

`dat` | A data frame. Each row represents principle components from different training datasets. Columns are genes used for PCA analysis.
`k` | The number of clusters used for hierarchical clustering
`n` | The number of top principle components from each datasets used for model building. Default is 20.
`cluster` | Provide pre-defined cluster membership of your data.
`study` | Under default (`TRUE`), studies involved in each cluster will be added in the output.

### Value

A named list of 6 elements is returned. It contains:

`cluster`

  A numeric vector on cluster membership of PCs

`size`

  A integer vector on the size of clusters

`avgLoading`

  A matrix of average loadings. Columns for clusters and rows for genes

`k`

  The number of clusters

`n`

  The number of top PCs used for clustering

`studies`

  A list of character vector containing studies in each cluster

### Examples

    data(miniAllZ)
    data(res_hcut)
    res <- buildAvgLoading(miniAllZ, k = 40, cluster = res_hcut$cluster)

[Package GenomicSuperSignature version 1.0.1 Index]