Class RNAseq
defines an RNAseq dataset.
countsRaw
matrix of raw counts (genes x cells). Recommended: Use gene IDs instead of gene Names.
CountsFeat
matrix (features x cells) indicating the number of no feature reads (row 1), ambiguous reads (row 2), low quality reads (row 3), unaligned reads (row 4) and others. The cellNames should be the same as in countsRaw.
metadata
matrix of metadata of all cells and genes (cells x features).
SpikeIn
If not NULL, contains logical vector with genes as names, where TRUE indicates that it's spike-in and FALSE indicates that it's a biological gene.
countsNorm
matrix of normalised counts (genes x cells).Recommended: Use gene IDs instead of gene Names.
CellsSizeFac
Contains size factors obtained in the normalisation.
cellsFailQC
List of cells that have failed QC.
genesHVG
Vector of highly variable genes.
pca
If not NULL, contains PCA results.
tsne
If not NULL, contains tSNE results.
difmap
If not NULL, contains diffusion map results.
clustering
If not NULL, contains information about potential clustering.
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