Phenotypes-class {gespeR} | R Documentation

## Phenotypes

### Description

Class used to represent various types of phenotypes, e.g. from siRNA-specific (SSP) or estimated gene-specific phenotypes (GSP).

### Usage

    Phenotypes(phenotypes, ...)

    ## S4 method for signature 'character'
    Phenotypes(phenotypes, type = c("SSP", "GSP"),
      sep = "\t", col.id = 1, col.score = 2)

    ## S4 method for signature 'cellHTS'
    Phenotypes(phenotypes, channel, sample)

    ## S4 method for signature 'Matrix'
    Phenotypes(phenotypes, ids = NULL, pnames = NULL,
      type = c("SSP", "GSP"))

### Arguments

`phenotypes` | The phenotypes as numeric vector, path to a .txt file with two columns (1: identifiers, 2: values), or a cellHTS object
`...` | Additional arguments
`type` | The type of phenotype (GSP, SSP)
`sep` | The separator string
`col.id` | Column number for the siRNA identifiers
`col.score` | Column number(s) for the phenotype score
`channel` | The cellHTS channel identifier
`sample` | The cellHTS sample index
`ids` | The siRNA/gene identifiers
`pnames` | The phenotype identifiers

### Value

A `Phenotypes` object

### Slots

`type`

  The type of represented phenotypes (i.e., "SSP" or "GSP")

`ids`

  The entity identifiers (i.e., siRNA or gene ids)

`pnames`

  The phenotype names

`values`

  The phenotypic values

### Author(s)

Fabian Schmich

### See Also

`plot.Phenotypes`

`join`

`gsp`

`ssp`

`scores`

`concordance`

### Examples

    phenos <- Phenotypes(system.file("extdata", "Phenotypes_screen_A.txt", package = "gespeR"),
    type = "SSP",
    col.id = 1,
    col.score = 2)

[Package gespeR version 1.10.1 Index]