Tech_OnescRNAseq: process one scRNAseq dataset to generate technical metadata

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

Description

Generate technical metadata for one single cell RNAseq dataset

Usage

Tech_OnescRNAseq(
  input,
  sf = 10000,
  mincounts = 500,
  mingenes = 200,
  maxmito = 0.2,
  mtRNA = "^mt-|^MT-",
  rRNA = "^Rp[sl][[:digit:]]|^RP[SL][[:digit:]]",
  chunk.size = NULL
)

Arguments

input	string of file or path name, a SingleCellExperiment or Seurat v3 object; input can be a string of the file name (or a URL starting http://, file://, etc.) of gene-by-cell count matrix, the rowname should be gene symbol; the file should be regular delimited file; Compressed files ending .gz and .bz2 are supported. input can be a string of the path name, which contains the barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz provided by 10X from CellRanger >=3.0 input can also be a SingleCellExperiment or a Seurat v3 object
sf	integer; Scale factor to normalize the single cell RNA-seq data (default: 10000)
mincounts	integer; the cutoff of filtering the cell if the total number of counts in the cell less than the mincounts (default:500)
mingenes	integer; the cutoff of filtering the cell if the total number of genes detected in the cell less than the mingenes (default: 200)
maxmito	float; the cutoff of filtering the cell if the percentage of mtRNA reads in the cell larger than the minmito; (default: 0.2);
mtRNA	string; the pattern of genenames for mitochondrial encoded RNAs ; (default: "^mt-|^MT-", the default is mtRNA genenames in human or mouse); If not human or mouse, input the gene name pattern of mtRNA
rRNA	string; the pattern of genenames for ribosomal proteins; (default: "^Rp[sl][[:digit:]]|^RP[SL][[:digit:]]", the default is ribosomal protein genenames in human or mouse); If not human or mouse, input the gene name pattern of ribosomal proteins
chunk.size	NULL or integer; default is NULL, suggesting data will be loaded into memory at one time, otherwise, the data will be loaded into memory by chunks with chunk.size

Value

a SingleCellExperiment object containing metadata for technical features

• assays; ShallowSimpleListAssays object containing two sparse matrix: counts and logcounts

• rowRanges@elementMetadata; A DataFrame containining metadata for each gene, including

  • ave.counts: the average counts

  • num.cells: the number of cells with the gene detected

• colData; A DataFrame containing metadata for each cell, including

  • log10_total_counts: the number of counts in each cell in log10 transformed

  • log10_total_features: the number of genes detected in each cell in log10 transformed

  • log10_total_counts_Mt: the number of mitochondrial counts in each cell in log10 transformed

  • log10_total_counts_rRNA: the number of rRNA counts in each cell in log10 transformed

• metadata: A list containing other metadata, including

  • rawmeta: a list of metadata for genes and cells of raw data before filtering, including

    • sf: normalization factor

    • ngenes: the number of genes

    • ncells: the number of cells

    • CellData: a dataframe containing metadata for each cell before filtering, includingtotal_counts,total_features,total_counts_Mt,total_counts_rRNA, pct_counts_rRNA (perentage of rRNA counts), pct_counts_Mt (percentage of mtRNA counts), libsize.drop(cell is filtered by library size), feature.drop (cell is filtered by the number of detected genes), mito.drop (cell is filtered by the mtRNA counts), is.drop (cell is filtered by either of library size, the number of genes or the mtRNA reads)

    • GeneData: a list containing the gene filter information (gene.keep, gene is filtered since none of the cells detect theg gene)

    • Cutoff: a list containing the cutoff values (count, gene, mito) for filtering cells

See Also

Process_OnescRNAseq , Bio_OnescRNAseq

Examples

library(scRNABatchQC)
sce<-Tech_OnescRNAseq(input="https://github.com/liuqivandy/scRNABatchQC/raw/master/bioplar1.csv.gz")
plotDensity(list(sce=sce))
names(sce@metadata)
head(sce@colData$log10_total_counts)

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