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Diffstat (limited to 'api')
| -rw-r--r-- | api/GN2-REST-API.md | 41 |
1 files changed, 40 insertions, 1 deletions
diff --git a/api/GN2-REST-API.md b/api/GN2-REST-API.md index fb6a691..17401f7 100644 --- a/api/GN2-REST-API.md +++ b/api/GN2-REST-API.md @@ -2,6 +2,29 @@ This document describes fetching data from GeneNetwork using the REST API. +Karl Broman wrote the [GNapi](https://github.com/kbroman/GNapi/blob/master/README.md) R package for accessing the GN API which allows convenient access: + +- `check_gn()` - Check connection. +- `list_species()` - List available species. +- `list_groups("drosophila")` - List available groups of datasets +- `list_datasets("BXD")` - List available datasets for a given group (here, `"BXD"`). +- `info_dataset("CB_M_1004_P")` - Get meta information about a data set. +- `info_datasets("B6D2F2")` - Get meta information about all data sets for a group. +- `info_pheno("BXD", "10038")` - Get summary information for a phenotype +- `get_pheno("BXD", "10646")` - Get phenotype values for a classical trait. +- `get_geno("BXD")` - Get genotypes for a group. +- `run_gemma("BXDPublish", "10015")` - Perform a genome scan with [gemma](https://github.com/genetics-statistics/GEMMA) +- `run_rqtl("BXDPublish", "10015")` - Perform a genome scan with [R/qtl](https://rqtl.org) +- `run_correlation("HC_M2_0606_P", "BXDPublish", "1427571_at")` - Finds traits that are correlated with a given trait. + +For further examples, see the [online +vignette](https://kbroman.org/GNapi/GNapi.html), which is also +available from within R: + +```r +vignette("GNapi") +``` + --- # Fetching Dataset/Trait info/data # --- @@ -24,7 +47,10 @@ curl http://genenetwork.org/api/v_pre1/species/mouse.json *For all queries where the last field is a user-specified name/ID, there will be the option to append a file format type. Currently there is only JSON (and it will default to JSON if none is provided), but other formats will be added later* -## Fetch Groups/RISets ## +## Groups + +The data is organised by group (also a drop down menu on the GN search page). General information on groups can be found [here](http://gn1.genenetwork.org/mouseCross.html). + This query can optionally filter by species: @@ -87,6 +113,19 @@ curl http://genenetwork.org/api/v_pre1/sample_data/HSNIH-PalmerPublish.csv Returns a CSV file with sample/strain names as the columns and trait IDs as rows +## Phenotype matrix + +``` +curl https://genenetwork.org/api/v_pre1/sample_data/BXDPublish.csv > BXDPublish.csv +``` + +You should query the API to get more information. Something like this +for the BXD + +``` +curl https://genenetwork.org/api/v_pre1/datasets/mouse/bxd > bxd_datasets.json +``` + ## Fetch Sample Data for Single Trait ## ``` curl http://genenetwork.org/api/v_pre1/sample_data/HC_M2_0606_P/1436869_at |