mathbiol/cbio

All you need is

<script src="https://mathbiol.github.io/cbio/cbio.js"></script>

Live at: https://mathbiol.github.io/cbio/

---

Experimenting with the possibility of having cBioPortal Web API as a client side JavaScript library. Since the API is not CORS enabled, a Google Script was implemented as a middle layer. The basic idea is to mimic the query syntax with objects constructed as

cbio.\( callbackFunction , { argument_i : value_i , ... } );

Many thanks to MSKCC's cBioPortal team - this is a great public service !

---

get

cbio.get = function(cmd,fun,parms)

All commands below are a type of bio.get, sy submitting command cmd to cbio WebAPI and process it through callback function fun with option parameters parms. For example

cbio.getTypesOfCancer()

is the same as

cbio.get('getTypesOfCancer')

and

cbio.getProteinArrayData(
	{
		case_set_id:"coadread_tcga_RPPA",
		array_info:1
	},
	function(x){console.log(cbio.table(x))}
)

is the same as

cbio.get(
	"getProteinArrayData",
	{
		case_set_id:"coadread_tcga_RPPA",
		array_info:1
	},
	function(x){console.log(cbio.table(x))}
)

or

cbio.get(
	"getProteinArrayData",
	function(x){console.log(cbio.table(x))},
	{
		case_set_id:"coadread_tcga_RPPA",
		array_info:1
	}
)

(note the code will check for switch over vars fun and parms)

getTypesOfCancer

cbio.getTypesOfCancer( callbackFunction );

example:

cbio.getTypesOfCancer()

getCancerStudies

cbio.getCancerStudies( callbackFunction );

example:

cbio.getCancerStudies()

getGeneticProfiles

cbio.getGeneticProfiles( "cancer study ID (required)" , callbackFunction)

example:

	cbio.getGeneticProfiles("gbm_tcga")

getCaseLists

cbio.getCaseLists(cancer_study_id)

example:

cbio.getCaseLists("gbm_tcga")

getProfileData

cbio.getProfileData({
	case_set_id: "case set ID (required)" ,
	genetic_profile_id: "one or more genetic profile IDs (required)",
	gene_list: "one or more HUGO Gene Symbols or Entrez Gene IDs (required)"
})

examples:

cbio.getProfileData({
	case_set_id:"gbm_tcga_all",
	genetic_profile_id:"gbm_tcga_mutations",
	gene_list:["BRCA1","BRCA2","TP53"]
})

cbio.getProfileData({
	case_set_id:"gbm_tcga_all",
	genetic_profile_id:["gbm_tcga_log2CNA","gbm_tcga_gistic"],
	gene_list:"EGFR"
})

getMutationData

cbio.getMutationData({
	genetic_profile_id: "one or more mutation profile IDs (required)",
	case_set_id: "case set ID (optional)",
	gene_list: "one or more HUGO Gene Symbols or Entrez Gene IDs (required)"
})

examples:

cbio.getMutationData({
	case_set_id:"gbm_tcga_all",
	genetic_profile_id:"gbm_tcga_mutations",
	gene_list:["EGFR","PTEN"]
})

cbio.getMutationData({
	genetic_profile_id:["ov_tcga_mutations","ucec_tcga_mutations"],
	gene_list:"BRCA1"
})

getClinicalData

cbio.getClinicalData("case set ID (required)")

example:

	cbio.getClinicalData("ov_tcga_all")

getProteinArrayInfo

cbio.getProteinArrayInfo({
	cancer_study_id: "cancer study ID (required)",
	protein_array_type:"protein_level or phosphorylation",
	 gene_list:["one or more HUGO Gene Symbols or Entrez Gene IDs"]
})

examples:

cbio.getProteinArrayInfo({cancer_study_id:"coadread_tcga"})

cbio.getProteinArrayInfo({
	cancer_study_id:"coadread_tcga",
	protein_array_type:"phosphorylation"
})

cbio.getProteinArrayInfo({
	cancer_study_id:"coadread_tcga",
	protein_array_type:"protein_level",
	gene_list:["ERBB2","TP53"]
})

getProteinArrayData

cbio.getProteinArrayData({
	case_set_id: "case set ID (required)",
	array_info: “[1 or 0]. If 1, antibody information will also be exported”
})

examples:

	cbio.getProteinArrayData("coadread_tcga_RPPA")

	cbio.getProteinArrayData({case_set_id:"coadread_tcga_RPPA"})

	cbio.getProteinArrayData({case_set_id:"coadread_tcga_RPPA",array_info:1})

---

getLinkStudy

cbio.getLinkStudy(parms)

example:

	cbio.getLinkStudy({cancer_study_id:"gbm_tcga",gene_list:["EGFR","NF1"]}) // returns URL

	cbio.getLinkStudy({cancer_study_id:"gbm_tcga",gene_list:["EGFR","NF1"]})  // opens URL

getLinkCase

cbio.getLinkCase(parms)

examples:

	cbio.getLinkCase({case_id:"TCGA-81-5910",cancer_study_id:"gbm_tcga"})  // returns URL

	cbio.getLinkCase({case_id:"TCGA-81-5910",cancer_study_id:"gbm_tcga"},'cbio')  // opens URL

oncoprint

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