Create a SingleCellExperiment object from files
importFromFiles(
assayFile,
annotFile = NULL,
featureFile = NULL,
assayName = "counts",
inputDataFrames = FALSE,
class = c("Matrix", "matrix"),
delayedArray = FALSE,
annotFileHeader = FALSE,
annotFileRowName = 1,
annotFileSep = "\t",
featureHeader = FALSE,
featureRowName = 1,
featureSep = "\t",
gzipped = "auto",
rowNamesDedup = TRUE
)
The path to a file in .mtx, .txt, .csv, .tab, or .tsv format.
The path to a text file that contains columns of annotation
information for each cell in the assayFile
. This file should have the
same number of rows as there are columns in the assayFile
. If multiple
samples are represented in the dataset, this should be denoted by a column
called 'sample'
within the annotFile
.
The path to a text file that contains columns of
annotation information for each gene in the count matrix. This file should
have the same genes in the same order as assayFile
. This is optional.
The name of the assay that you are uploading. The default
is "counts"
.
If TRUE
, assayFile
, annotFile
and
featureFile
should be data.frames
object (or its inheritance)
instead of file paths. The default is 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
.
Whether there's a header (colnames) in the cell
annotation file. Default is FALSE
.
Which column is used as the rownames for the cell
annotation file. This should match to the colnames of the assayFile
.
Default is 1
(first column).
Separater used for the cell annotation file. Default is
"\t"
.
Whether there's a header (colnames) in the feature
annotation file. Default is FALSE
.
Which column is used as the rownames for the feature
annotation file. This should match to the rownames of the assayFile
.
Default is 1
. (first column).
Separater used for the feature annotation file. Default is
"\t"
.
Whether the input file is gzipped. Default is "auto"
and it will automatically detect whether the file is gzipped. Other options
are TRUE
or FALSE
.
Boolean. Whether to deduplicate rownames. Default
TRUE
.
a SingleCellExperiment object
Creates a SingleCellExperiment object from a counts file in various formats, and files of cell and feature annotation.