importDropEst {singleCellTK} | R Documentation

## Create a SingleCellExperiment Object from DropEst output

### Description

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.

### Usage

    importDropEst(
      sampleDirs = NULL,
      dataType = c("filtered", "raw"),
      rdsFileName = "cell.counts",
      sampleNames = NULL,
      delayedArray = FALSE
    )

### Arguments

`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 `FALSE`.

### Details

`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

### Value

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

### Examples

    # 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')

[Package singleCellTK version 2.2.0 Index]