validateConfig: Validate Parameter List

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

Description

validateConfig validates a list of parameter key/value pairs.

Usage

validateConfig(parameters)

Arguments

parameters

A list containing key/value pairs which define the parameters for the analysis (see importConfig for more information).

Details

validateConfig takes a list of key/value pairs which represent the parameters for the analysis, validates them and then returns the validated parameter key/value list.

Required key/value pairs are:

counts_directory

Directory where count data files are located.

targets_file

Location of targets file which contains the mapping files and experimental conditions.

results_directory

Directory where results directory will 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_file key [Default: 0]

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

Value

A list containing the validated parameters.

See Also

Other configuration functions: buildConfig, importConfig, writeConfig

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

Examples

 # Basic parameter list
 params <- list ( 'counts_directory' = "/path/to/counts.txt",
                  'targets_file'     = "/path/to/targets.txt",
                  'results_directory' = "/path/to/result_dir")

 # Validate parameters
 validateConfig(params)

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