makeMinimalSingleEndReadDataset: Makes a minimal single end dataset

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

Makes a minimal single end dataset

Description

Makes a minimal single end dataset by combining the arguments to a data.frame. You have to switch directory to the root of the data store first.

Usage

makeMinimalSingleEndReadDataset(
  fqDir,
  species = "",
  adapter1 = "GATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
  strandMode = "both",
  readCount = NULL,
  dataRoot = DEFAULT_DATA_ROOT
)

makeMinimalPairedEndReadDataset(
  fqDir,
  species = "",
  adapter1 = "GATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
  adapter2 = "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT",
  strandMode = "both",
  readCount = NULL,
  readTypeSuffix = c("_R1.fastq.gz", "_R2.fastq.gz"),
  dataRoot = DEFAULT_DATA_ROOT
)

Arguments

fqDir	a character specifying the path to the directory holding the fastq files. The paths stored in the dataset will be relative to the dataRoot
species	a character specifying the species name.
adapter1	a character representing the adapter sequence.
strandMode	a character specifying the strand mode for the dataset.
dataRoot	a string specifying the root directory of the data
adapter2	a character representing the second adapter sequence in the case of a paired end dataset.

Value

Returns a data.frame containing the provided information.

Functions

• makeMinimalPairedEndReadDataset(): Does the same for paired end reads.

Author(s)

Rehrauer, Hubert

Schmid, Peter

Examples

fqDir = system.file("extdata/yeast_10k", package="ezRun", mustWork=TRUE)
species = "Example"
ds = makeMinimalSingleEndReadDataset(fqDir, species)
ds2 = makeMinimalPairedEndReadDataset(fqDir, species)

uzh/ezRun documentation built on March 5, 2025, 3:41 p.m.