extractDownstreamStatistics: Extract downstream statistics

In rajewsky-lab/dropbead: dropbead

Description

Extract downstream basic statistics such as cell number, median numger of reads, genes, UMIs per cell. The data.table package is used for fast reading of the DGE matrices.

Usage

extractDownstreamStatistics(object, dge.name = NULL, reads.by.cell = NULL,
  min.umi = 250, read.stats = NULL)

Arguments

object	The exact location of the folder containing the analyzed data.
dge.name	The file containing the DGE. If none is provided, the function assumes that DGE is stored under the name dge.txt.gz.
reads.by.cell	The data.frame containing the reads per cell. If none is provided, the function tries to read the file out_readcounts.txt.gz.
min.umi	The minimum number of UMIs to keep a cell and not discard it.
read.stats	A data.frame containing read statistics, as it is produced by the function extractReadStatistics.

rajewsky-lab/dropbead documentation built on May 26, 2019, 10 p.m.