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diff --git a/api_readme.md b/api_readme.md index d0102d67..96e8b246 100644 --- a/api_readme.md +++ b/api_readme.md @@ -1,5 +1,7 @@ # API Query Documentation # - +--- +# Fetching Dataset/Trait info/data # +--- ## Fetch Species List ## To get a list of species with data available in GN (and their associated names and ids): @@ -98,14 +100,52 @@ curl http://gn2-zach.genenetwork.org/api/v_pre1/trait/BXD/10001 { "additive": 2.39444435069444, "id": 4, "locus": "rs48756159", "lrs": 13.4974911471087 } ``` +--- + +# Analyses # +--- +## Mapping ## +Currently two mapping tools can be used - GEMMA and R/qtl. qtlreaper will be added later with Christian Fischer's RUST implementation - https://github.com/chfi/rust-qtlreaper + +Each method's query takes the following parameters respectively (more will be added): +### GEMMA ### +* trait_id (*required*) - ID for trait being mapped +* db (*required*) - DB name for trait above (Short_Abbreviation listed when you query for datasets) +* use_loco - Whether to use LOCO (leave one chromosome out) method (default = false) +* maf - minor allele frequency (default = 0.01) + +Example query: +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/mapping?trait_id=10015&db=BXDPublish&method=gemma&use_loco=true +``` + +### R/qtl ### +(See the R/qtl guide for information on some of these options - http://www.rqtl.org/manual/qtl-manual.pdf) +* trait_id (*required*) - ID for trait being mapped +* db (*required*) - DB name for trait above (Short_Abbreviation listed when you query for datasets) +* rqtl_method - hk (default) | ehk | em | imp | mr | mr-imp | mr-argmax ; Corresponds to the "method" option for the R/qtl scanone function. +* rqtl_model - normal (default) | binary | 2-part | np ; corresponds to the "model" option for the R/qtl scanone function +* num_perm - number of permutations; 0 by default +* control_marker - Name of marker to use as control; this relies on the user knowing the name of the marker they want to use as a covariate +* interval_mapping - Whether to use interval mapping; "false" by default +* pair_scan - *NYI* + +Example query: +``` +curl http://gn2-zach.genenetwork.org/api/v_pre1/mapping?trait_id=1418701_at&db=HC_M2_0606_P&method=rqtl&num_perm=100 +``` + +Some combinations of methods/models may not make sense. The R/qtl manual should be referred to for any questions on its use (specifically the scanone function in this case) + ## Calculate Correlation ## -Currently only Pearson Sample and Tissue correlations are implemented +Currently only Sample and Tissue correlations are implemented This query currently takes the following parameters (though more will be added): * trait_id (*required*) - ID for trait used for correlation * db (*required*) - DB name for the trait above (this is the Short_Abbreviation listed when you query for datasets) * target_db (*required*) - Target DB name to be correlated against -* type - Sample or Tissue (default = Sample) +* type - sample (default) | tissue +* method - pearson (default) | spearman * return - Number of results to return (default = 500) Example query: |