Description Usage Arguments Details Value Examples
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.
1 2 3 4 5 6 7 8 9 10 11 |
seqcDirs |
A vector of paths to seqc 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 |
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. |
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 |
cbNotFirstCol |
Boolean. |
feNotFirstCol |
Boolean. |
combinedSample |
Boolean. If |
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.
A SingleCellExperiment
object containing the combined count
matrix, the feature annotations, and the cell annotation.
1 2 3 4 5 6 7 8 9 10 11 | # 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)
|
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