testDrops: Determine whether droplets are cells or blank drops in an...

In jacobheng/cellwrangler: Supplemental toolkit for single-cell RNAseq analysis

Description

testDrops() is a wrapper function around the emptyDrops() function in the excellent SoupX package. Returns a list object consisting of a results dataframe from the emptyDrops() function, as well as barcodes of cells and empty droplets.

Usage

testDrops(raw_exprs_mtx, lower_UMI_threshold = 100,
  upper_UMI_threshold = 500, test.ambient = T, FDR = 0.01,
  niters = 10000)

Arguments

raw_exprs_mtx	a raw expression matrix created with the cellranger pipeline; rows are genes and columns are barcodes
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
test.ambient	A logical scalar indicating whether results should be returned for barcodes with totals less than or equal to lower_UMI_threshold.
FDR	numeric; parameter for the testDrops function. FDR value to use in the testDrops function when statistically determining cells vs non-cells
niters	An integer scalar specifying the number of iterations to use for the Monte Carlo p-value calculations.

Value

a testDrops object with a results dataframe, cell_barcodes, and blank_barcodes

Examples

testDrops_res <- testDrops(raw_exprs_mtx, lower_UMI_threshold=100, upper_UMI_threshold=500, 
test.ambient=T, FDR=0.01, niters=10000)

jacobheng/cellwrangler documentation built on Aug. 12, 2019, 6:49 a.m.