dsReadStats: Read cell barcode statistics produced by Dropseq pipeline

Description Usage Arguments Value

View source: R/dropseq-dge.R

Description

The Dropseq pipeline produces output summary files that describe the number of genes, UMIs, and reads per cell barcode. This reads them in from several files and collates them into a single data.table.

Usage

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dsReadStats(
  dge.summary.reports,
  cell.readcount.reports = NULL,
  sample.names,
  name.cells.with.sample = T
)

Arguments

dge.summary.reports

(Character vector) Paths of DGE report files. (These files typically end with the suffix ".report_dge.summary.txt")

cell.readcount.reports

(Character vector) Paths of cell readcount reports for getting number of reads per cell. (These files typically end with the suffix ".report_cell_readcounts.txt.gz")

sample.names

(Character vector) Names of samples.

name.cells.with.sample

(Logical) Convert cell barcodes to cell names?

Value

Returns a data.frame with cells as rows, and metadata as columns.


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