calcNormLoadings: Calculate loadings for each factor
In rliger: Linked Inference of Genomic Experimental Relationships

calcNormLoadings

R Documentation

Calculate loadings for each factor

Description

Calculates the contribution of each factor of W,V, and U to the reconstruction.

Usage

calcNormLoadings(object)

Arguments

object

liger object. Should call quantileNorm before calling.

Value

A dataframe, such that each column represents the contribution of a specific matrix (W, V_1, V_2, etc. )

Examples

ligerex <- createLiger(list(ctrl = ctrl, stim = stim))
ligerex <- normalize(ligerex)
ligerex <- selectGenes(ligerex)
ligerex <- scaleNotCenter(ligerex)
# Minimum specification for fast example pass
ligerex <- optimizeALS(ligerex, k = 5, max.iters = 1)
ligerex <- quantile_norm(ligerex)
calcNormLoadings(ligerex)

rliger documentation built on Nov. 9, 2023, 1:07 a.m.