ProteinTableR6: Protein Table

In protViz/SRMService: Report Quantitative Mass Spectrometry Data

Description

Protein Table

Protein Table

Public fields

data

data.frame with colnames sample ID rownames proteinID

experimentID

name of the experiment

Active bindings

experimentID

name of the experiment

Methods

Public methods

• ProteinTableR6$new()

• ProteinTableR6$set_data_wide()

• ProteinTableR6$get_protein_id()

• ProteinTableR6$get_data_long()

• ProteinTableR6$get_all_long()

• ProteinTableR6$get_data_wide()

• ProteinTableR6$get_annotation()

• ProteinTableR6$clone()

---

Method new()

Usage

ProteinTableR6$new(
  annotation,
  proteinID = "proteinID",
  required = c("NrPeptides", "Fasta.Headers")
)

---

Method set_data_wide()

Usage

ProteinTableR6$set_data_wide(data)

---

Method get_protein_id()

Usage

ProteinTableR6$get_protein_id()

---

Method get_data_long()

Usage

ProteinTableR6$get_data_long()

---

Method get_all_long()

Usage

ProteinTableR6$get_all_long()

---

Method get_data_wide()

Usage

ProteinTableR6$get_data_wide()

---

Method get_annotation()

Usage

ProteinTableR6$get_annotation()

---

Method clone()

The objects of this class are cloneable with this method.

Usage

ProteinTableR6$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

library(SRMService)
x <- data.frame(Raw.file = c("A","B","C"),"MeasurementOrder" = c(1,2,3) , Gender = c("F","F","M"))
cm <- Annotation$new(x, experimentID = "E1 fixed Gender", fixed = "Gender")
dataProt <- data.frame("proteinID" = c("P1","P2","P3"), NrPeptides = c(1,2,3), "Fasta.Headers" = rep("",3), "A" = rexp(3), "B" = rexp(3), "C" = rexp(3))
length(dplyr::intersect("Annotation",class(dataProt))) > 0
cm$sampleID
pt <- ProteinTableR6$new(cm)
pt$set_data_wide(dataProt)
pt$get_data_long()
pt$get_data_wide()
pt$get_all_long()

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