KallistoMetadata-class {BgeeCall} | R Documentation

## 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.

[Package BgeeCall version 1.8.0 Index]