read_ms_dge_summary: Read mixed-species DGE summary files

In argschwind/dropseqr: Utilities for Drop-seq data processing

Description

Read summary files created DigitalExpression from Drop-seq tools for a species mixing experiment. Creates data.frame containing merged summary for all cell barcodes present in both summary files. For instructions on how to generate DGE files for species-mixing experiments, see the Drop-seq alignment cookbook provided by the [McCarroll lab](http://mccarrolllab.com/dropseq/).

Usage

read_ms_dge_summary(summary_files, species = c("SPECIES1", "SPECIES2"),
  stringsAsFactors = default.stringsAsFactors())

Arguments

summary_files	Character vector specifying the paths to DigitalExpression summary files for each species. Must be of length two as only species mixing experiments with two species are supported.
species	Character vector of length two providing the species names that should be used for creating output.
stringsAsFactors	Logical: should character vectors be converted to factors? Typically only applies to cell barcodes.

Value

A data.frame containing containing summary data on all cell barcodes found in summary files of both species.

Examples

## Not run: 
library(dropseqr)

# read two summary files and merge into one data.frame
infiles <- c("./human_summary.txt", "/mouse_summary.txt")
x <- read_ms_dge_summary(infiles, species = c("human", "mouse"))

## End(Not run)

argschwind/dropseqr documentation built on May 23, 2019, 4:24 p.m.