Bio_OnescRNAseq: process one scRNAseq dataset to generate biological metadata

In liuqivandy/scRNABatchQC: a package for quality control of multiple single cell RNAseq data

Description

Generate metadata (HVGs, PC-related genes, pathways) for one single cell RNAseq represented by gene-cell count table

Usage

Bio_OnescRNAseq(
  scdata,
  nHVGs = 1000,
  nPCs = 10,
  PCind = 1,
  organism = "mmusculus"
)

Arguments

scdata	a SingleCellExperiment object; (results from Tech_OnescRNAseq
nHVGs	integer; the number of highly variable genes (default: 1000)
nPCs	integer: the number of principal components (default: 10)
PCind	integer; which principal component for exploring biological featues (default: 1; the first principal component will be used to find genes highly correlated with PCA 1); PCind should be less than nPC
organism	string; the organism of single cell RNAseq datasets; if supported by WebGestaltR, functional enrichment analysis will be performed (defeault: mmusculus)

Value

a new SingleCellExperiment object by adding features into the the elementMetadata and metadata slots of the input object:

• rowRanges@elementMetadata;

  • hvg: a dataframe containing mean, variance and z-score for dispersion

  • genevar_by_tounts: variance explained by the log-transformed counts

  • genevar_by_features: variance explained by the log-transformed features

  • genevar_by_Mt: variance explained by the log-transformed mitochondrial counts

  • genevar_by_rRNA: variance explained by the log-transformed rRNA counts

• metadata: A list containing other metadata, including

  • pc1genes: a dataframe containing the genes highly correlated with the 1st (default) or the PCind principal component

  • pc1Pathway: a dataframe containing the pathways enriched in pc1 (default) or the PCind genes

  • hvgPathway: a dataframe containing the pathways enriched in top n (default:1000) highly variable genes

See Also

Process_OnescRNAseq , Tech_OnescRNAseq

Examples

library(scRNABatchQC)
sce<-Tech_OnescRNAseq(input="https://github.com/liuqivandy/scRNABatchQC/raw/master/bioplar1.csv.gz")
sce<-Bio_OnescRNAseq(sce)
head(sce@rowRanges@elementMetadata)
sce@metadata$hvgPathway

liuqivandy/scRNABatchQC documentation built on March 24, 2021, 11:01 p.m.