Annotation: Condition Map

In protViz/SRMService: Report Quantitative Mass Spectrometry Data

Description

Condition Map

Condition Map

Methods

Public methods

• Annotation$new()

• Annotation$exists()

• Annotation$levels()

• Annotation$get()

• Annotation$get_factors()

• Annotation$get_sample_id()

• Annotation$as_numeric()

• Annotation$get_color()

• Annotation$clone()

---

Method new()

Usage

Annotation$new(
  annotation,
  experimentID,
  fixed = NULL,
  random = NULL,
  sampleID = "Raw.file"
)

---

Method exists()

Usage

Annotation$exists(colname)

---

Method levels()

Usage

Annotation$levels(colname)

---

Method get()

Usage

Annotation$get(colname)

---

Method get_factors()

Usage

Annotation$get_factors()

---

Method get_sample_id()

Usage

Annotation$get_sample_id()

---

Method as_numeric()

Usage

Annotation$as_numeric(colname)

---

Method get_color()

Usage

Annotation$get_color(
  colname,
  pal_function = dichromat_pal,
  pal_name = "BrowntoBlue.10"
)

---

Method clone()

The objects of this class are cloneable with this method.

Usage

Annotation$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

library(SRMService)
library(dplyr)
x <- data.frame(Raw.file = c("A","B","C"),"MeasurementOrder" = c(1,2,3) , Gender = c("F","F","M"))
cm <- Annotation$new(x, experimentID = "E1 with random Effect", fixed = "Gender", random="MeasurementOrder")
cm$exists("Gender")
cm$exists("Stop")
cm$fixed
cm$random
cm$as_numeric("Gender")
cm$levels("Gender")
cm$get("Gender")
cm$get_color("Gender")
cm$sampleID
cm$get_sample_id()
cm$annotation

protViz/SRMService documentation built on Nov. 13, 2021, 9:58 a.m.