View source: R/importBUStools.R
importBUStools | R Documentation |
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
)
BUStoolsDirs |
A vector of paths to BUStools output files. Each sample
should have its own path. For example: |
samples |
A vector of user-defined sample names for the samples to be
imported. Must have the same length as |
matrixFileNames |
Filenames for the Market Exchange Format (MEX) sparse
matrix files (.mtx files). Must have length 1 or the same
length as |
featuresFileNames |
Filenames for the feature annotation files.
Must have length 1 or the same length as |
barcodesFileNames |
Filenames for the cell barcode list file.
Must have length 1 or the same length as |
gzipped |
Boolean. |
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 |
rowNamesDedup |
Boolean. Whether to deduplicate rownames. Default
|
A SingleCellExperiment
object containing the count
matrix, the gene annotation, and the cell annotation.
# 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")
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.