importTargets: Read Targets File

In sanger-pathogens/deago: DEAGO: RNASeq differential expression analysis and GO term enrichment reporter

Description

importTargets reads a delimited targets file into a dataframe.

Usage

importTargets(file, path = NULL, sep = "\t")

Arguments

file	A character string giving the name of the file.
path	A character string giving the directory containing the file. This may be omitted if the file is in the current working directory.
sep	A character used to separate the fields.

Details

The targets file is a text file which contains information about the RNA samples, linking their experimental conditions to their count data files. Rows correspond to samples and columns to their respective count data file locations and the experimental conditions that were applied. By default, it is expected that the targets file will be tab-delimited but, other delimiters can be used if specified using sep.

The targets file must contain at least three columns with the following, column names:

filename

name of the file containing the count data for the sample

condition

experimental treatment or condition that was applied

replicate

replicate identifier - can be numeric or character

importTargets adds a label column which contains labels generated using the condition and replicate values for the sample to use in plots.

Value

dataframe: containing the target information and labels

See Also

Other target functions: validateTargets

Other import functions: annotateDataset, importAnnotation, importConfig, readCountData, validateConfig, validateTargets

Examples

## Not run: 
 # Import tab-delimited targets file from working directory
 importTargets("targets.txt")

 # Import tab-delimited targets file from another directory
 importTargets("targets.txt", path="/path/to/targets")

 # Import comma-delimited targets file from working directory
 importTargets("targets.txt", sep=",")

## End(Not run)

sanger-pathogens/deago documentation built on May 28, 2019, 8:42 a.m.