Construct SCE object from seqc output — importSEQC • singleCellTK

Read the filtered barcodes, features, and matrices for all samples from (preferably a single run of) seqc output. Import and combine them as one big SingleCellExperiment object.

importSEQC(
  seqcDirs = NULL,
  samples = NULL,
  prefix = NULL,
  gzipped = FALSE,
  class = c("Matrix", "matrix"),
  delayedArray = FALSE,
  cbNotFirstCol = TRUE,
  feNotFirstCol = TRUE,
  combinedSample = TRUE,
  rowNamesDedup = TRUE
)

Arguments

seqcDirs: A vector of paths to seqc output files. Each sample should have its own path. For example: "./pbmc_1k_50x50". Must have the same length as samples.
samples: A vector of user-defined sample names for the samples to be imported. Must have the same length as seqcDirs.
prefix: A vector containing the prefix of file names within each sample directory. It cannot be null and the vector should have the same length as samples.
gzipped: Boolean. TRUE if the seqc output files (sparse_counts_barcode.csv, sparse_counts_genes.csv, and sparse_molecule_counts.mtx) were gzip compressed. FALSE otherwise. Default seqc outputs are not gzipped. Default FALSE.
class: Character. The class of the expression matrix stored in the SCE object. Can be one of "Matrix" (as returned by readMM function), or "matrix" (as returned by matrix function). Default "Matrix".
delayedArray: Boolean. Whether to read the expression matrix as DelayedArray object or not. Default FALSE.
cbNotFirstCol: Boolean. TRUE if first column of sparse_counts_barcode.csv is row index and it will be removed. FALSE the first column will be kept.
feNotFirstCol: Boolean. TRUE if first column of sparse_counts_genes.csv is row index and it will be removed. FALSE the first column will be kept.
combinedSample: Boolean. If TRUE, importSEQC returns a SingleCellExperiment object containing the combined count matrix, feature annotations and the cell annotations. If FALSE, importSEQC returns a list containing multiple SingleCellExperiment objects. Each SingleCellExperiment contains count matrix, feature annotations and cell annotations for each sample.
rowNamesDedup: Boolean. Whether to deduplicate rownames. Only applied if combinedSample is TRUE or only one seqcDirs specified. Default TRUE.

Value

A SingleCellExperiment object containing the combined count matrix, the feature annotations, and the cell annotation.

Details

importSEQC imports output from seqc. The default sparse_counts_barcode.csv or sparse_counts_genes.csv from seqc output contains two columns. The first column is row index and the second column is cell-barcode or gene symbol. importSEQC will remove first column. Alternatively, user can call cbNotFirstCol or feNotFirstCol as FALSE to keep the first column of these files. When combinedSample is TRUE, importSEQC will combined count matrix with genes detected in at least one sample.

Examples

# Example #1
# The following filtered feature, cell, and matrix files were downloaded from
# https://support.10xgenomics.com/single-cell-gene-expression/datasets/
# 3.0.0/pbmc_1k_v3
# The top 50 hg38 genes are included in this example.
# Only the top 50 cells are included.
sce <- importSEQC(
    seqcDirs = system.file("extdata/pbmc_1k_50x50", package = "singleCellTK"),
    samples = "pbmc_1k_50x50",
    prefix = "pbmc_1k",
    combinedSample = FALSE)