Description Usage Arguments Value Examples
normaliseDGE
normalise a gene by cell matrix
1 2 3 |
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 |
A matrix of read counts
1 | # normalised_counts <- normalise_dge(dge)
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