datafileTemplate: (Empty) template data file which summarises the data to be...

In nixstix/RNASeqAnalysis: Analysis of RNA-Seq data: QC filtering, expression analysis, differential expression pipeline

Description

This is an empty dataset, the purpose of which is to act as a template for users. In the data file, the name of the file, the name of the sample and the technical replicate, and whether the sample is paired-end or single-end should be included. In addition, if the user is planning to filter the input file (see runQAandFilter), a column is provided for the user to add the name of the output fastq file.

This data file acts as input to many of the package's functions. The format of the data file should not be altered, save to add observations (rows).

The data set datafileExample is an example of a data file containing observations.

Usage

datafileTemplate

Format

a dataframe with 0 observations of 5 vairables

Details

• File. The name of the fastq (fastq.gz) file to be processed

• PE. "PE" should be entered into this column if the sample is from a paired-end run, or "SE" if the sample is from a single-end run.

• Sample. The name of the sample (e.g. "control", "lung").

• Replicate. The name of the replicate (e.g. "a", "2").

• FilteredFile. The name of the fastq (fastq.gz) file that the results from runQAandFilter function are written to.

Author(s)

Nicky Thrupp [e-mail]

nixstix/RNASeqAnalysis documentation built on May 23, 2019, 7:06 p.m.