ReadAndFilter10xData | R Documentation |
Reads in 10X files using Read10X and filters abberent cells using PerformEmptyDropletFiltering and returns a Seurat object.
ReadAndFilter10xData(
dataDir,
datasetId,
datasetName = NULL,
emptyDropNIters = 10000,
emptyDropsFdrThreshold = 0.001,
storeGeneIds = TRUE,
emptyDropsLower = 100,
useEmptyDropsCellRanger = FALSE,
nExpectedCells = 8000,
useSoupX = FALSE,
previouslyFilteredMatrix = NULL
)
dataDir |
Either the directory holding raw count data (generally the raw_feature_bc_matrix), or the parent 'outs' dir from cellranger |
datasetId |
This will be used as a prefix for barcodes, and stored in metadata. Also used as the project name for the Seurat object. |
datasetName |
An optional print-friendly name that will be stored in metadata |
emptyDropNIters |
The number of iterations to use with PerformEmptyDrops() |
emptyDropsFdrThreshold |
The FDR threshold to call cells in emptyDrops() |
storeGeneIds |
If true, a map to translate geneId and name (by default rownames will use gene name) |
emptyDropsLower |
Passed directly to emptyDrops(). The lower bound on the total UMI count, at or below which all barcodes are assumed to correspond to empty droplets. |
useEmptyDropsCellRanger |
If TRUE, will use DropletUtils emptyDropsCellRanger instead of emptyDrops |
nExpectedCells |
Only applied if emptyDropsCellRanger is selected. Passed to n.expected.cells argument |
useSoupX |
If true, SoupX will be run against the run input data, instead of emptyDrops |
previouslyFilteredMatrix |
An optional filepath to a pre-filtered count matrix in h5 format. If non-null, this file will be read instead of dataDir. Empty drops and/or soupX will be skipped. |
A Seurat object.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.