RNAseq-class: Class RNAseq

Description Slots

Description

Class RNAseq defines an RNAseq dataset.

Slots

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.


BPijuanSala/proSeq documentation built on Oct. 10, 2018, 7:20 p.m.