create_monocle_cds: Create a monocle CellDataSet object from a directory of...
In jacobheng/cellwrangler: Supplemental toolkit for single-cell RNAseq analysis

Description Usage Arguments Value Examples

create_monocle_cds() creates a monocle CellDataSet object from a directory of 10X Genomics scRNAseq data created using the cellranger pipeline. Includes options to determine which barcodes are cells vs non-cells in the original raw matrix.

create_monocle_cds(cellranger_outs_path, cellranger_v3 = T,
  which_matrix = "raw", UMI_cutoff = NULL, testDrops = F,
  lower_UMI_threshold = 100, upper_UMI_threshold = 500, FDR = 0.01,
  cell_barcodes = NULL)

`cellranger_outs_path`	the path to the "outs" directory in the cellranger library folder e.g. "/mycellranger_library/outs"
`cellranger_v3`	logical; if cellranger version 3 and above was used to produced matrices.
`which_matrix`	must be "raw" or "filtered" to specify the raw or filtered matrix to load respectively.
`UMI_cutoff`	numeric; a single cutoff of total UMI counts per cell to use for determining cells (i.e. all barcodes with total UMI counts above this cutoff will be included in the expression matrix); defaults to NULL
`testDrops`	logical; whether to use the testDrops function to determine which barcodes are cells (and therefore included in the expression matrix)
`lower_UMI_threshold`	numeric; parameter for the testDrops function. All barcodes with total UMI counts below this value are considered empty droplets (i.e. not cells)
`upper_UMI_threshold`	numeric; parameter for the testDrops function. All barcodes with total UMI counts above this value are considered cells
`FDR`	numeric; parameter for the testDrops function. FDR value to use in the testDrops function when statistically determining cells vs non-cells
`cell_barcodes`	a vector of barcodes to use for creating the expression matrix (all barcodes specified by cell_barcodes are assumed to be cells)

a monocle CellDataSet object

1 2	dat <- create_monocle_cds(cellranger_outs_path, cellranger_filter= F, UMI_cutoff=NULL, testDrops=T, lower_UMI_threshold=100, upper_UMI_threshold=500, FDR=0.01, cell_barcodes=NULL)