importConfig: Read Configuration File

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

Description

importConfig reads configuration file into a list.

Usage

importConfig(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

importConfig reads a tab-delimited configuration file containing key/value pairs which represent the parameters for the analysis into a list. The configuration file should contain two columns, the first containing the keys outlined below and the second, their values.

Required key/value pairs are:

counts_directory

Directory where count data files are located.

targets_file

Location of targets file containing the mappings between file names and experimental conditions.

results_directory

Location where results directory is to be created.

Other accepted key/value pairs and their defaults are:

gene_ids

Name of column in count files which contains the gene identifiers [Default: geneID]

alpha

Significance cut-off, see results for more information [Default: 0.05]

control

Name of condition in the targets file which was the control [Default: control]

annotation_file

Location of annotation file, see annotateDataset [Default: NULL]

keep_images

Give a value of 1 to keep images which are used in the HTML report, see plotToFile for more information [Default: 0]

qc_only

Give a value of 0 to run DESeq2 analysis functions or a value of 1 to report only the QC plots [Default: 1]

go_analysis

Give a value of 1 to run GO term enrichment analysis using topGO. If value of 1 given for go_analysis, an annotation file must be provided as a value for the annotation key [Default: 0]

Parameters are validated using validateConfig.

importConfig returns a list containing the parameter values with the names corresponding to their keys.

Value

A key/value list containing the parameters from the configuration file.

See Also

Other configuration functions: buildConfig, validateConfig, writeConfig

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

Examples

## Not run: 
 # Import tab-delimited config from working directory
 importConfig("config.txt")

 # Import tab-delimited config from another directory
 importConfig("config.txt", path="/path/to/config")

 # Import comma-delimited config from working directory
 importConfig("config.txt", sep=",")

## End(Not run)

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