Expression Queries

• List Matrix
• Get Matrix Information
• Get Matrix
• Read Matrix
• Get Profile
• TFA Profile

List Matrix

Gets the list of uploaded expression matrices.

Params

type: string,  // ='list-expression'

Return

!Array<{
  fileName: string,
  matrixName: string,
  description: string
}>

Get Matrix Information

Gets the expression matrix information, with given matrix name.

Params

type: string,       // ='expression-info'
matrixName: string  // Matrix Name of the expression matrix.

Return

{
  allGeneNames: !Object<string>,       // All row labels
  allConditionNames: !Object<string>,  // All column labels
  allValueMin: number,                 // of all matrix values
  allValueMax: number
}

Get Matrix

Gets the expression matrix, with given genes and experiment conditions.

Params

type: string,                   // ='expression'
matrixName: string,             // Matrix Name of the expression matrix.
geneNames: !Array<string>,      // Name list selecting the genes (rows).
conditionNames: !Array<string>  // Name list selecting the experiment conditions (columns).

Return

{
  values: Array<Array<number>>,    // 2D matrix data
  geneNames: !Array<string>,       // As row labels
  conditionNames: !Array<string>,  // As column labels
  valueMin: number,                // of values in selected rows and columns
  valueMax: number
}

Read Matrix

bowen: DUPLICATE WITH GET MATRIX? need to combine them

Gets the expression matrix, with given genes and experiment conditions.

Params

type: string,           // ='read-expression'
fileName: string,       // File name of the expression matrix.
geneRegex: string,      // Regex selecting the genes (rows).
conditionRegex: string  // Regex selecting the experiment conditions (columns).

Return

{
  values: Array<Array<number>>,  // 2D matrix data
  valueMin: number,              // of values in selected rows and columns
  valueMax: number,
  allValueMin: number,           // of all matrix valuse
  allValueMax: number,
  geneNames: !Array<string>,     // As row labels
  conditionNames: !Array<string> // As column labels
}

Profile

Gets the profile data for selected genes.

Params

type: string,                   // ='profile'
matrixName: string,             // Matrix Name of the expression matrix.
geneNames: !Array<string>,      // Name list selecting the genes (rows).
conditionNames: !Array<string>  // Name list selecting the experiment conditions (columns).

Return

{
  values: Array<Array<number>>,    // 2D profile data
  geneNames: !Array<string>,       // As row labels
  conditionNames: !Array<string>,  // As column labels
  valueMin: number,                // of values in selected rows and columns
  valueMax: number
}

TFA Profile

Gets the TFA profile data for selected genes.

Params

type: string,                   // ='tfa-profile'
matrixName: string,             // Matrix Name of the expression matrix.
geneNames: !Array<string>,      // Name list selecting the genes (rows).
conditionNames: !Array<string>  // Name list selecting the experiment conditions (columns).

Return

{
  tfaValues: !Array<{
    index: number,                 // column index. TFA values exist for a subset of values.
    value: number
  }>,
  geneNames: !Array<string>,       // As row labels
  conditionNames: !Array<string>,  // As column labels
  valueMin: number,                // of values in selected rows and columns
  valueMax: number
}