Phenotypes-class: Phenotypes

In cbg-ethz/gespeR: Gene-Specific Phenotype EstimatoR

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)

cbg-ethz/gespeR documentation built on May 13, 2019, 2:02 p.m.