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

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(gespeR)
Loading required package: ggplot2
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/gespeR/Phenotypes-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Phenotypes-class
> ### Title: Phenotypes
> ### Aliases: Phenotypes Phenotypes,Matrix-method Phenotypes,cellHTS-method
> ###   Phenotypes,character-method Phenotypes-class
> 
> ### ** Examples
> 
> phenos <- Phenotypes(system.file("extdata", "Phenotypes_screen_A.txt", package = "gespeR"),
+ type = "SSP",
+ col.id = 1,
+ col.score = 2)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>