Construct SCE object from BUStools output — importBUStools • singleCellTK

Read the barcodes, features (genes), and matrix from BUStools output. Import them as one SingleCellExperiment object. Note the cells in the output files for BUStools 0.39.4 are not filtered.

importBUStools(
  BUStoolsDirs,
  samples,
  matrixFileNames = "genes.mtx",
  featuresFileNames = "genes.genes.txt",
  barcodesFileNames = "genes.barcodes.txt",
  gzipped = "auto",
  class = c("Matrix", "matrix"),
  delayedArray = FALSE,
  rowNamesDedup = TRUE
)

Arguments

BUStoolsDirs: A vector of paths to BUStools output files. Each sample should have its own path. For example: ./genecount. 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 BUStoolsDirs.
matrixFileNames: Filenames for the Market Exchange Format (MEX) sparse matrix files (.mtx files). Must have length 1 or the same length as samples.
featuresFileNames: Filenames for the feature annotation files. Must have length 1 or the same length as samples.
barcodesFileNames: Filenames for the cell barcode list file. Must have length 1 or the same length as samples.
gzipped: Boolean. TRUE if the BUStools output files (barcodes.txt, genes.txt, and genes.mtx) were gzip compressed. FALSE otherwise. This is FALSE in BUStools 0.39.4. Default "auto" which automatically detects if the files are gzip compressed. Must have length 1 or the same length as samples.
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-class object or not. Default FALSE.
rowNamesDedup: Boolean. Whether to deduplicate rownames. Default TRUE.

Value

A SingleCellExperiment object containing the count matrix, the gene annotation, and the cell annotation.

Examples

# Example #1
# FASTQ files were downloaded from
# https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0
# /pbmc_1k_v3
# They were concatenated as follows:
# cat pbmc_1k_v3_S1_L001_R1_001.fastq.gz pbmc_1k_v3_S1_L002_R1_001.fastq.gz >
# pbmc_1k_v3_R1.fastq.gz
# cat pbmc_1k_v3_S1_L001_R2_001.fastq.gz pbmc_1k_v3_S1_L002_R2_001.fastq.gz >
# pbmc_1k_v3_R2.fastq.gz
# The following BUStools command generates the gene, cell, and
# matrix files

# bustools correct -w ./3M-february-2018.txt -p output.bus | \
#   bustools sort -T tmp/ -t 4 -p - | \
#   bustools count -o genecount/genes \
#     -g ./transcripts_to_genes.txt \
#     -e matrix.ec \
#     -t transcripts.txt \
#     --genecounts -

# The top 20 genes and the first 20 cells are included in this example.
sce <- importBUStools(
  BUStoolsDirs = system.file("extdata/BUStools_PBMC_1k_v3_20x20/genecount/",
    package = "singleCellTK"),
  samples = "PBMC_1k_v3_20x20")