PBMC_metaData: PBMC 4K meta data

In constantAmateur/SoupX: Single Cell mRNA Soup eXterminator

PBMC 4K meta data

Description

Collection of bits of meta data relating to the 10X PBMC 4K data.

Usage

data(PBMC_metaData)

Format

PBMC_metaData is a data.frame with 4 columns: RD1, RD2, Cluster, and Annotation.

Details

This data set pertains to the 10X demonstration PBMC 4K data and includes metadata about it in the data.frame named PBMC_metaData.

PBMC_metaData was created using Seurat (v2) to calculate a tSNE representation of the data and cluster cells with these commands.

• set.seed(1)

• srat = CreateSeuratObject(sc$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_metaData = as.data.frame(srat@dr$[e-mail])

• colnames(PBMC_metaData) = c('RD1','RD2')

• PBMC_metaData$Cluster = factor([e-mail][rownames(PBMC_metaData),'res.1'])

• PBMC_metaData$Annotation = factor(c('7'='B','4'='B','1'='T_CD4','2'='T_CD4','3'='T_CD8','5'='T_CD8','6'='NK','8'='NK','0'='MNP','9'='MNP','10'='MNP','11'='?')[as.character(PBMC_metaData$Cluster)])

Source

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

constantAmateur/SoupX documentation built on Nov. 2, 2022, 10:16 a.m.