AbundanceMetadata-class: AbundanceMetadata s4 class

In BgeeDB/BgeeCall: Automatic RNA-Seq present/absent gene expression calls generation

AbundanceMetadata s4 class

Description

An S4 class that is the parent class of all abundance tool Classes. It contains information needed to all abundance tools. This class can be seen as an abstract class, you should never instanciate it.

Slots

txOut

Similar to tximport txOut parameter. Allows to keep abundance at transcript level if TRUE (default = FALSE)

ignoreTxVersion

logical used to remove transcript version in transcript ID if TRUE (default = FALSE)

cutoff_type

Defines the approach used to generate present/absent calls. default value is 'pValue', allowing calls to be generated using a pValue. Other possible values are 'intergenic' allowing to use a ratio of intergenic sequences considered as present as a threshold, or use qValue allowing calls to be generated from a qValue.

cutoff

numeric value of the cutoff used to generate the present/absent calls. If value of the slot cutoff_type is 'pValue' this cutoff will correspond to the highest pValue allowing to define a gene as present. If value of the slot cutoff_type is 'intergenic' this cutoff will correspond to the proportion of intergenic present divided by proportion of protein coding present. If value of the slot cutoff_type is 'qValue' this cutoff will correspond to the highest qValue allowing to define a gene as present. The qValue is calculated based on the proportion of intergenic/(intergenic + genic) at each unique abundance value (TPM). The default value is 0.05. Be careful when modifying this value as it could have a huge impact on present/absent calls.

full_transcriptome_file

Name of the fasta file containing both transcriptomic and intergenic regions. This file is created by the pipeline. You should edit this slot only if you already have such a file with a different name.

tx2gene_file

Name of the file containing the mapping between transcript IDs and gene IDs (See the tximport package vignette for more details). This file is created by the pipeline. You should edit this slot only if you already have such a file with a different name. This file must be store at get_species_path()

tx2gene_file_without_version

Name of the file containing the mapping between transcript IDs and gene IDs if ignoreTxVersion == TRUE (See the tximport package vignette for more details). This file is created by the pipeline. You should edit this slot only if you already have such a file with a different name. This file must be store at get_species_path()

gene2biotype_file

Name of the file containing the mapping between gene IDs and biotypes. This file is created by the pipeline. You should edit this slot only if you already have such a file with a different name.

tool_name

Name of the tool that will be use to generate transcript abundance estimation. All descendant of this class have to define a value for this slot (in the prototype section)

abundance_file

Name of the transcript-level abundance file. All descendant of this class have to define a value for this slot (in the prototype section)

read_size_kmer_threshold

read size of the library below which transcript index is created using a smaller kmer size

transcript_id_header

Name of the header of the column that contains transcript ID

count_header

Name of the header of the column that contains count

abundance_header

Name of the header of the column that contains abundance

eff_length_header

Name of the header of the column that contains effective length

transcript_calls_file_name

default name of file containing all transcript ids and calls (if calls created at transcript level)

gene_calls_file_name

default name of file containing all gene ids and calls (if calls created at gene level)

transcript_cutoff_file_name

default name of file containing summary of cutoff used to generate transcript expression calls (if calls created at transcript level)

gene_cutoff_file_name

default name of file containing summary of cutoff used to generate gene expression calls (if calls created at gene level)

transcript_distribution_file_name

default name of density plot file containing TPM distribution of all transcripts (if calls created at transcript level)

gene_distribution_file_name

default name of density plot file containing TPM distribution of all genes (if calls created at gene level)

BgeeDB/BgeeCall documentation built on Nov. 10, 2023, 5:40 a.m.