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.
importDropEst( sampleDirs = NULL, dataType = c("filtered", "raw"), rdsFileName = "cell.counts", sampleNames = NULL, delayedArray = FALSE )
| sampleDirs | A path to the directory containing the data files. Default "./". |
|---|---|
| dataType | can be "filtered" or "raw". Default |
| rdsFileName | File name prefix of the DropEst RDS output. default is "cell.counts" |
| sampleNames | A User-defined sample name. This will be prepended to all cell barcode IDs. Default "sample". |
| delayedArray | Boolean. Whether to read the expression matrix as
DelayedArray object or not. Default |
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')