importDropEst: Create a SingleCellExperiment Object from DropEst output
In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Description Usage Arguments Details Value Examples

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 = TRUE
)

`sampleDirs`	A path to the directory containing the data files. Default "./".
`dataType`	can be "filtered" or "raw". Default `"filtered"`.
`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 `TRUE`.

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

A SingleCellExperiment object containing the count matrix, the feature annotations from DropEst as ColData, and any metadata from DropEst

# 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')