Phenotypes-class: Phenotypes

Description Usage Arguments Value Slots Author(s) See Also Examples

Description

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

Usage

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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

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


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