txCutoffPlot: Plot Cumulative Distribution of Reads per Cell Barcode

In farrellja/URD: URD

Description

To determine the number of cells recovered in a Dropseq sample, the cumulative distribution of the number of reads recovered per unique cell barcode is plotted. The elbow in the curve suggests the boundary between "real cells" with many reads and "ambient RNA" that has bound to the remainder of the beads (which have few reads). The 10X pipeline determines which barcodes constitute 'cells' in a different fashion, but this produces an equivalent

Usage

txCutoffPlot(
  tx.reads.per.cell = NULL,
  molecule.info.path = NULL,
  n.cells = NULL,
  main = "",
  xmax = 5000
)

Arguments

n.cells	(Numeric) Draw a line at putative number of cells to use downstream
main	(Character) Title for the plot
xmax	(Numeric) Max value of plot x-axis
gz.in	(Character) Path to Dropseq cell read counts report (".report_cell_readcounts.txt.gz")

farrellja/URD documentation built on June 17, 2020, 4:48 a.m.