imports the RDS file created by DropEst (https://github.com/hms-dbmi/dropEst) and create a SingleCellExperiment object from either the raw or filtered counts matrix. Additionally parse through the RDS to obtain appropriate feature annotations as SCE coldata, in addition to any metadata.
A path to the directory containing the data files. Default "./".
can be "filtered" or "raw". Default "filtered"
.
File name prefix of the DropEst RDS output. default is "cell.counts"
A User-defined sample name. This will be prepended to all cell barcode IDs. Default "sample".
Boolean. Whether to read the expression matrix as
DelayedArray object or not. 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 deduplicate rownames. Default
TRUE
.
A SingleCellExperiment
object containing the count matrix,
the feature annotations from DropEst as ColData, and any metadata from DropEst
importDropEst
expects either raw counts matrix stored as "cm_raw" or filtered
counts matrix stored as "cm" in the DropEst rds output.
ColData is obtained from the DropEst corresponding to "mean_reads_per_umi","aligned_reads_per_cell",
"aligned_umis_per_cell","requested_umis_per_cb","requested_reads_per_cb"
If using filtered counts matrix, the colData dataframe is
subset to contain features from the filtered counts matrix alone.
If any annotations of ("saturation_info","merge_targets","reads_per_umi_per_cell") are
found in the DropEst rds, they will be added to the SCE metadata field
# Example results were generated as per instructions from the developers of dropEst described in
# https://github.com/hms-dbmi/dropEst/blob/master/examples/EXAMPLES.md
sce <- importDropEst(sampleDirs = system.file("extdata/dropEst_scg71", package = "singleCellTK"),
sampleNames = 'scg71')