buildAvgLoading: Calculate average loadings of each cluster

In shbrief/PCAGenomicSignatures: Interpretation of RNA-seq experiments through robust, efficient comparison to public databases

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)

shbrief/PCAGenomicSignatures documentation built on May 3, 2023, 11:21 a.m.