mixt

package
v0.0.0-...-15b8e4a Latest Latest
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Published: Mar 6, 2018 License: MIT Imports: 10 Imported by: 0

Documentation

Index

Constants

This section is empty.

Variables

Functions

func ClinicalEigengene

func ClinicalEigengene(tissue string) ([]byte, error)

func ClinicalROI

func ClinicalROI(tissue string) ([]byte, error)

func ClinicalRanksum

func ClinicalRanksum(tissue, cohort string) ([]byte, error)

func CohortBoxplot

func CohortBoxplot(module, orderByTissue, orderByModule, cohort string) (string, error)

func CohortHeatmap

func CohortHeatmap(tissue, module, cohort string) (string, error)

func CohortScatterplot

func CohortScatterplot(tissueA, tissueB, moduleA, moduleB, cohort string) (string, error)

func EigengeneCorrelation

func EigengeneCorrelation(tissueA, tissueB string) ([]byte, error)

func GeneListCSV

func GeneListCSV(modules []string, tissue string) ([]byte, error)

func GeneOverlapTest

func GeneOverlapTest(tissueA, tissueB string) ([]byte, error)

func Get

func Get(key, filetype string) ([]byte, error)

func GetAllModuleNames

func GetAllModuleNames(gene string) ([]string, error)

func GetCohorts

func GetCohorts() ([]string, error)

func GetCommonGOTermGenes

func GetCommonGOTermGenes(module, tissue, id string) ([]string, error)

func GetCommonGenes

func GetCommonGenes(tissue, module, geneset, status string) ([]string, error)

func GetCommonUserERGenes

func GetCommonUserERGenes(module, tissue string, genelist []string) ([]string, error)

func GetGOTermNames

func GetGOTermNames() ([]string, error)

func GetGeneSetNames

func GetGeneSetNames() ([]string, error)

func GetGenes

func GetGenes() ([]string, error)

func GetSlice

func GetSlice(pkg, fun, args string) ([]string, error)

func GetTOMGraph

func GetTOMGraph(tissue, component, format string) ([]byte, error)

func GetTissues

func GetTissues() ([]string, error)

func Heatmap

func Heatmap(tissue, module string) (string, error)

func HeatmapReOrder

func HeatmapReOrder(tissue, module, orderByTissue, orderByModule, cohort string) (string, error)

func Init

func Init(addr, username, password string)

func ModuleHypergeometricTest

func ModuleHypergeometricTest(tissueA, tissueB string) ([]byte, error)

func PatientRankCorrelation

func PatientRankCorrelation(tissueA, tissueB string) ([]byte, error)

func PatientRankSum

func PatientRankSum(tissueA, tissueB, cohort string) ([]byte, error)

func ROITest

func ROITest(tissueA, tissueB string) ([]byte, error)

Types

type Analyses

type Analyses struct {
	Ranksum []float64 `json:"ranksum"`
	Overlap []float64 `json:"overlap"`
	Common  []string  `json:"common"`
}

func ModuleComparisonAnalyses

func ModuleComparisonAnalyses(tissueA, tissueB, moduleA, moduleB string) (Analyses, error)

type ByName

type ByName []Module

func (ByName) Len

func (a ByName) Len() int

func (ByName) Less

func (a ByName) Less(i, j int) bool

func (ByName) Swap

func (a ByName) Swap(i, j int)

type EnrichmentScores

type EnrichmentScores struct {
	Sets map[string][]Set
}

func GetEnrichmentScores

func GetEnrichmentScores(module, tissue string) (enrichment EnrichmentScores, err error)

type GOTerm

type GOTerm struct {
	GOId           string `json:"GO.ID"`
	Term           string
	Annotated      int
	Significant    int
	Expected       float64
	ClassicFisher  string `json:"classicFisher"`
	Weight01Fisher string `json:"weight01Fisher"`
	Rank           int    `json:"Rank in weight01Fisher"`
	Module         string `json:"module"`
}

func GetGOScoresForTissue

func GetGOScoresForTissue(tissue, goterm string) ([]GOTerm, error)

func GetGOTerms

func GetGOTerms(module, tissue string, terms []string) ([]GOTerm, error)

type Gene

type Gene struct {
	Name        string
	Correlation string
	K           float64
	Kin         float64
	Updown      string
}

func GetGeneList

func GetGeneList(module, tissue string) (genes []Gene, url string,
	err error)

type Module

type Module struct {
	Name                  string
	Tissue                string
	HeatmapUrl            string
	AlternativeHeatmapUrl string
	Genes                 []Gene
	EnrichmentScores      EnrichmentScores
	GOTerms               []GOTerm
	Url                   string
	ScatterplotUrl        string
	BoxplotUrl            string
}

func GetModule

func GetModule(name, tissue, cohort string) (Module, error)

func GetModules

func GetModules(tissue string) ([]Module, error)

type ModuleScores

type ModuleScores struct {
	// contains filtered or unexported fields
}

type Response

type Response struct {
	Item string
}

type Score

type Score struct {
	Set          string  `json:"sig.set"`
	Name         string  `json:"_row"`
	Size         int     `json:"sig.size,string"`
	UpDownCommon int     `json:"updn.common,string"`
	UpDownPvalue float64 `json:"updn.pval,string"`
	UpCommon     int     `json:"up.common,string"`
	UpPvalue     float64 `json:"up.pval,string"`
	DownCommon   int     `json:"dn.common,string"`
	DownPvalue   float64 `json:"dn.pval,string"`
	Tissue       string  `json:"tissue,omitempty"`
}

func GetEnrichmentForTissue

func GetEnrichmentForTissue(tissue, geneset string) ([]Score, error)

func GetEnrichmentScore

func GetEnrichmentScore(module, tissue, geneset string) (Score, error)

type Set

type Set struct {
	SetName       string
	SignatureName string
	Size          int
	UpDownCommon  int
	UpDownPvalue  float64
	UpCommon      int
	UpPvalue      float64
	DownCommon    int
	DownPvalue    float64
}

type UserScore

type UserScore struct {
	PValue float64  `json:"p_values"`
	Module string   `json:"module"`
	Common []string `json:"common"`
}

func UserEnrichmentScores

func UserEnrichmentScores(tissue string, genelist []string) ([]UserScore, error)

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