calc_pca: Calculate principal components using irlba

Description Usage Arguments Value

View source: R/dims.R

Description

Calculate principal components using irlba

Usage

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calc_pca(fce, expt = "sce", assay = "logcounts", genes = NULL,
  n_pcs = 20, scale = TRUE)

Arguments

fce

fce object

expt

one of either sce (rna data, the default) or fsce (functional data)

assay

select which assay data to use for PCA, defaults to logcounts (i.e. log normalized data)

genes

vector of genes to include in PCA, defaults to all genes

n_pcs

number of principle components to return

scale

perform PCA on input on scaled data, defaults to TRUE

Value

fce object with PCA values added to reducedDims


hesselberthlab/scrunchy documentation built on Dec. 7, 2018, 7:55 a.m.