EpivizFeatureData-class: 'EpivizFeatureData' objects
In epiviz/epivizr-tmp: R Interface to epiviz web app

Description Details Fields Methods Author(s)

Encapsulate data for genomic features

The object field is constrained to be SummarizedExperiment. Data is obtained from columns of a determined assay. Measurement names are checked against the row names of the colData slot. The rowData is assumed to be a GIntervalTree object, its mcols must contain columns PROBEID and SYMBOL.

assay:: (integer or character) indicating assay from which data is obtained

: .checkColumns(columns): Checks columns are a subset of names(colData(object)).
: .getColumns(): Returns names(colData(object)).
: plot(): Calls the scatterPlot method of EpivizDeviceMgr-class with the first measurements in columns as x and y.
: getMeasurements(): Returns named character vector. Entries are of format '<name>$<column>'. Vector names are of format '<id>__<column>'.
: parseMeasurement(msId): Parses measurement of format '<id>__<column>'.
: packageData(msId): Get data for msId for rows overlapping curQuery. Returns a list with components: min: min value for data range, max: max value for data range, data: list with slots: gene: from SYMBOL column of mcols(rowData(object)), start: feature start position, end: feature end position, probe: from PROBEID column of mcols(rowData(object)), value: numeric data value.