Description Functions related to the description of the metadata variables Functions related to the SVD of a matrix Eigen vectors and their relationship with the metadata variables
The snorm package provides three categories of functions: functions related to the description of the metadata variables, singular value decomposition of the data matrix and relationship between the eigenvectors and the variables of the metadata.
Function summaryTable
provides a summary description for every
variable (column) in the metadata (statistics such as mean, median, maximum, mean
and the number of missing cases are provided). Function variablesRelation
provides a table with correlation P values and statistic estimates for each pair
of the variables in the metadata. This helps to understand whether any technical
variables are related to the variables of interest.
Function fs
performs Singular Value Decomposition (SVD) on a
data matrix (using fast.svd
function) and
transforms the matrix D to reflect percent variance explained. Function
plotVariance
plots the percent variance explained. Function
matrixOutliers
creates a scatterplot of the matrix
columns corresponding to the most extreme values of the first eigen
vector of the SVD.
Function eigenVariable
calculates an overall ANOVA P value for
the relationship between the eigen vectors and the variables in the
metadata. Function eigenVariablePlot
plots a variable from the
metadata against an eigen vector. Function pcScatter
creates a
scatter plot of the first two eigen vectors and colors the point by a variable
from the metadata. Function geneOntology
creates a basic unit
to obtain MF, BP and CC categories from GO for a gene list.
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