KallistoMetadata-class: KallistoMetadata S4 class

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

KallistoMetadata S4 class

Description

An S4 class that is the desendant of the AbundanceMetadata class. It contains all metadata needed to run kallisto analysis. All slots of this class have a default value. You do not need to edit them to run the package

Slots

download_kallisto

A logical allowing to use an already installed version of kallisto or to download a version that will be used only by this package

kallisto_windows_url

URL to the binary of kallisto for windows

kallisto_linux_url

URL to the binary of kallisto for linux

kallisto_osx_url

URL to the binary of kallisto for MacOS

kallisto_windows_dir

Name of the directory where kallisto will be installed on windows

kallisto_linux_dir

Name of the directory where kallisto will be installed on linux

kallisto_osx_dir

Name of the directory where kallisto will be installed on Mac

unix_kallisto_name

Name of the kallisto executable in linux and macOS

windows_kallisto_name

Name of the kallisto executable in windows

index_file

Name of index file generated by kallisto with default kmer size. It will be generated using the fasta file that contains both transcriptomic and intergenic regions. Do not use an index you generated outside of this package. 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_tool_path()

k15_index_file

same as index_file. This index is generated with smallest kmers and will be used only for libraries containing reads smallest than 50nt.

single_end_parameters

kallisto parameters used to run a single end mapping

pair_end_parameters

kallisto parameters used to run a pair end mapping

overwrite_index

logical allowing to overwrite already existing index. FALSE by default. Then by default already existing index files will not be generated again.

overwrite_quant

logical allowing to overwrite already existing abundance.txt files. FALSE by default. Then by default already existing quantitfdication files will not be generated again.

overwrite_calls

logical allowing to overwrite already existing present/absent calls. FALSE by default. Then by default already generated calls will not be generated again.

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