GEVAInput-class {geva} | R Documentation

## GEVA Input Data

### Description

The `GEVAInput` class contains the initial data for `GEVA` usage. It stores numeric matrices of logFC values from differential expression comparison results. Options for calculations and summarizing are also included.

### Value

A `GEVAInput` object

### Slots

`values`

  `numeric matrix` (m*n) of log-ratio values, usually logFC

`weights`

  `numeric matrix` (m*n) of weighted values. If not defined, all weight values are equal to 1

`factors`

  `factor` (n elements) representing the grouping of the n columns. If not defined, all factors are equal to `NA`

`ftable`

  `data.frame` with m rows containing attribute columns associated to the features (e.g., probes or genes)

`info`

  `list` of supplementary information related to the input

### Methods

Alternative accessors

`levels(x)`

  Returns the unique values from the assigned factors; or `NA` if there are no assigned factors in `x`

Conversion and coercion

`as.array(x, ...)`

  Converts this object to `array`

Dimension accessors

`dim(x)`

  Gets the dimensions defined for both matrices in `values` and `weights` slots

`dimnames(x) <- value`

  Sets the `list` with the row and column names.
  Individual dimension names can also be set using `rownames<-` and `colnames<-`

`dimnames(x)`

  Gets a `list` with the row and column names.
  Individual dimension names can also be accessed through `rownames` and `colnames`

`inputnames(object)`

  Gets the input column names (same as `colnames(object)`)

`length(x)`

  Returns the number of rows in the `values` slot

`names(x)`

  Same as `inputnames`. For internal use

Plotting

`plot(x, y, ...)`

  Summarizes the input using the default parameters, then calls the plot on the returned `GEVASummary` object.
  Not intended to regular use and will give a warning if called

Properties

`analysis.params(gobject)`

  Returns a `list` of analysis parameters passed to `geva.merge.input` or `geva.read.tables` to obtain this object

Subsetting

`head(x, n = 6L, ...)`

  Returns the first parts of the `values` table

`tail(x, n = 6L, ...)`

  Returns the last parts of the `values` table

[Package geva version 1.0.0 Index]