PBMC_DR: tSNE coordinates for PBMC data

Description Usage Format Details Source

Description

tSNE coordinates for PBMC 4k data used in the vignette. tSNE have been calculated using standard Seurat settings. Also includes a column indicating which Seurat cluster each cell belongs to.

Usage

1

Format

Note that cells have been named assuming the PBMC4k channel is named "Channel1". A data frame with 4,340 rows (one per cell) and 3 variables:

RD1

The first tSNE coordinate

RD2

The second tSNE coordinate

Cluster

A factor giving cluster assignment

Details

The full list of commands used to create this object (assuming scl is a SoupChannelList object containing the PBMC4k data): set.seed(1) srat = CreateSeuratObject(scl$toc) srat = NormalizeData(srat) srat = ScaleData(srat) srat = FindVariableGenes(srat) srat = RunPCA(srat,pcs.compute=30) srat = RunTSNE(srat,dims.use=seq(30)) srat = FindClusters(srat,dims.use=seq(30),resolution=1) PBMC_DR = as.data.frame([email protected][email protected]) colnames(PBMC_DR) = c('RD1','RD2') PBMC_DR$Cluster = factor([email protected][rownames(PBMC_DR),'res.1'])

Source

https://support.10xgenomics.com/single-cell-gene-expression/datasets/2.1.0/pbmc4k


constantAmateur/SoupX documentation built on July 23, 2018, 9:20 a.m.