UserMetadata S4 class

Description

An S4 class containing all metadata that have to be provided by the user It is mandatory to edit 'species_id', 'rnaseq_lib_path', 'transcriptome_path', 'annotation_name', 'annotation_object' and potentialy 'run_ids' before using the package.

Slots

species_id

The NCBI Taxon Id of the species

run_ids

A vector of charater. Has to be provided only if a subset of runs present in UserMetadata@rnaseq_lib_path has to be run. If empty, all fastq files present in the rnaseq_lib_path will be considered as technical replicates and merged to run one transcript expression estimation analyse.

reads_size

The size of the reads. If smaller than 'KallistoMetadata@read_size_kmer_threshold', an index with a kmer size of 15 bp will be used.

rnaseq_lib_path

Path to the directory of the RNA-Seq library that contains fastq files. The extension of the fastq files name must be .fq, .fastq, .fq.gz, or .fastq.gz

transcriptome_name

Name of the transcriptome used to generate arborescence of output repositories.

transcriptome_object

Object containing transcriptome

annotation_name

Name of the annotation used to generate arborescence of output repositories.

annotation_object

Object containing annotations from GTF or GFF file

working_path

Working directory. By default the working directory is defined with the 'getwd()' function.

gtf_source

The source name from where the gtf file comes from. By default is ensembl.

simple_arborescence

logical allowing to create a simple arborescence of directory. If 'TRUE' (default), all results will be on the same directory (working_path/intergenic_release/all_results/libraryId). Use 'FALSE' if you plan to generate expression calls for the same library using different transcriptomes or gene annotations, otherwise you will overwrite previous results. When 'FALSE' the path to result folder looks like : working_path/intergenic_release/speciesId/kallisto/transcriptome_name/annotation_name/libraryId

output_dir

(optional) Allows to manually define your output directory. By default the path to output directory is created automatically from the working_path (working_path/intergenic_release/all_results/libraryId/).

verbose

logical allowing to use the verbose mode. TRUE by default.

custom_intergenic_path

path to a local version of reference intergenic fasta file. If NULL (by default) the reference intergenic fasta file will be downloaded. If not NULL BgeeCall will merge this local reference intergenic file with the transcriptome. Except if you generated your own intergenic regions always keep it NULL.

encrypted_pattern

Allows to manage encrypted libraries. If a fastq file with the suffix .enc is found for a run, this slot will allow to use a string pattern to decrypt it. . This encrypted_pattern needs to contain the string FASTQ_PATH that will be transformed to the actual path to the fastq file.