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
)
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
.
A vector of user-defined sample names for the samples to be
imported. Must have the same length as seqcDirs
.
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.
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
.
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"
.
Boolean. Whether to read the expression matrix as
DelayedArray object or not. Default FALSE
.
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.
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.
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.
Boolean. Whether to deduplicate rownames. Only applied
if combinedSample
is TRUE
or only one seqcDirs
specified. Default TRUE
.
A SingleCellExperiment
object containing the combined count
matrix, the feature annotations, and the cell annotation.
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.
# 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)