normaliseDGE: Normalise Digital Gene Expression Matrix

Description Usage Arguments Value Examples

Description

normaliseDGE normalise a gene by cell matrix

Usage

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normaliseDGE(dge, verbose = FALSE, center = TRUE, scale = TRUE,
  outliers = FALSE, threshold = 5, min_library_size = 200,
  gene_subset = 0.5, transformation = "sqrt")

Arguments

dge

matrix; a digital gene expression matrix containing count data (columns = cells, rows = genes), can be a sparce Matrix object.

verbose

logical; if TRUE the function will print diagnostic graphs along the way

center

logical; if true genes are centered to mean of 0

scale

logical; if TRUE genes are scaled to unit variance

outliers

logical; calculate max value per gene and cell to assess threshold position

threshold

integer; any normalised values larger than this will be rounded down

min_library_size

real; only cells with library size equal or greater to this will be kept

gene_subset

real; what fraction of the genes do you want to keep (by mean) e.g. 0.5 is top half most expressed

transformation

character; either sqrt (default) or asinh

Value

A matrix of read counts

Examples

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# normalised_counts <- normalise_dge(dge)

marchinilab/dropsim documentation built on May 17, 2019, 1:34 p.m.