produce_deliverables | R Documentation |
The goal of this function is to parse the variaus infos tables and to produce and save the results in a standardized object and directories format.
produce_deliverables(
dir_kallisto,
anno,
infos_tables,
analysis_level = "both",
file_type = "h5",
digits = 4,
ignoreTxVersion = TRUE,
counts = TRUE,
add_volcano_labels = NULL,
report_filename = NULL,
outdir = "deliverables",
r_objects = "r_objects",
force = FALSE,
ncores = 1,
verbose = FALSE
)
dir_kallisto |
Directory with Kallisto quantifications |
anno |
Path to the anno file matching the reference used for the Kallisto analysis |
infos_tables |
A |
analysis_level |
Should the analysis be done at the "gene", "tx" or "both" level. Default: "both". |
file_type |
Abundance file format to use (h5 or tsv). |
digits |
Integer indicating the number of decimal places |
ignoreTxVersion |
Should the version number in the IDs be ignored
during import. Default: |
counts |
Save count tables in the <outdir>/counts folder? Default:
|
add_volcano_labels |
Add labels to volcano plots. Must be either
|
report_filename |
The name of the report that will be saved in the
|
outdir |
A |
r_objects |
A |
force |
Should the files be re-created if they already exists? Default:
|
ncores |
Number of cores to use for de analysis. Default |
verbose |
Print progression of the analysis? Default: |
add_volcanos_labels |
A vector of the symbols to show on the volcano
plots. If |
The results will be returned as a list with the following slots:
* txi$gene: The txi object at the gene level. * txi$tx: The txi object at the transcript level. * counts$gene: A list of count matrices at the gene level matching the count matrices found in the txi object. * counts$tx: A list of count matrices at the transcript level matching the count matrices found in the txi object. * pca$gene: The list of PCA ggplot objects at the gene level. * pca$tx: The list of PCA ggplot objects at the transcript level. * de$gene: The list of DE results in the gene format. * de$tx: The list of DE results in the transcript format. * de$volcano$gene: The volcano plots produced at the gene level. * de$volcano$tx: The volcano plots produced at the transcript level. * de$report: The lines of the report. * de$infos_tables: The infos tables used to produce the results.
It's the content of the infos_tables that will determine which deliverables will be produced. Some tables are mandatory for other steps to be performed. DE analysis requires de_infos and design_infos tables. Volcano analysis requires the DE analysis to also be performed beforehand.
Invisibly returns a list
that contains all the results.
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