Commit 14030369 authored by liiskolb's avatar liiskolb
Browse files

vignette

parent c2584825
......@@ -297,7 +297,7 @@ publish_gosttable(multi_gostres1,
filename = NULL)
```
### Data sources
### Data sources and versions
Available data sources and their abbreviations are:
......@@ -311,6 +311,7 @@ Available data sources and their abbreviations are:
* [CORUM](https://mips.helmholtz-muenchen.de/corum/) (CORUM)
* [Human phenotype ontology](https://hpo.jax.org/) (HP)
### Custom data sources with `upload_GMT_file`
In addition to the available GO, KEGG, etc data sources, users can upload their own custom data source using the Gene Matrix Transposed file format (GMT). The file format is described in [here](https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29). The users can compose the files themselves or use pre-compiled gene sets from available dedicated websites like Molecular Signatures Database ([MSigDB](http://software.broadinstitute.org/gsea/msigdb/genesets.jsp)), etc. The GMT files for g:Profiler default sources (except for KEGG and Transfac as we are restricted by data source licenses) are downloadabale from the Data sources section in [g:Profiler](https://biit.cs.ut.ee/gprofiler/gost).
......@@ -318,7 +319,7 @@ In addition to the available GO, KEGG, etc data sources, users can upload their
`upload_GMT_file` enables to upload GMT file(s). The input `gmtfile` is the filename of the GMT file together with the path to the file. The input can also be several GMT files compressed into a ZIP file.
The file extension should be **.gmt** or **.zip** in case of multiple GMT files. The uploaded filename is used to define the source name in the enrichment results.
For example, using the BioCarta gene sets downloaded from the [MSigDB Collections](http://software.broadinstitute.org/gsea/msigdb/collections.jsp#C7)
For example, using the BioCarta gene sets downloaded from the [MSigDB Collections](http://software.broadinstitute.org/gsea/msigdb/collections.jsp#C7).
```{r eval = F}
download.file(url = "http://software.broadinstitute.org/gsea/resources/msigdb/7.0/c2.cp.biocarta.v7.0.symbols.gmt", destfile = "extdata/biocarta.gmt")
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