read_ms_dge_files: Read mixed-species DGE files

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

Description

Read DGE files created DigitalExpression from Drop-seq tools for a species mixing experiment. Creates data.frame containing merged DGE data for all cell barcodes present in both DGE 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_files(dge_files, species = c("SPECIES1", "SPECIES2"),
  stringsAsFactors = default.stringsAsFactors())

Arguments

dge_files	Character vector specifying the paths to DigitalExpression output 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 gene names.

Value

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

Examples

## Not run: 
library(dropseqr)

# read two dge files and merge into one data.frame
infiles <- c("./human_dge.txt", "/mouse_dge.txt")
x <- read_ms_dge_files(infiles, species = c("human", "mouse"))

## End(Not run)

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