ProteinAnnotation: Decorates LFQData with a row annotation and some protein...

In wolski/prolfqua: Proteomics Label Free Quantification

Decorates LFQData with a row annotation and some protein specific functions.

Description

Decorates LFQData with a row annotation and some protein specific functions.

Decorates LFQData with a row annotation and some protein specific functions.

Public fields

row_annot

data.frame containing further information

pID

column with protein ids

description

name of column containing descriptions

cleaned_ids

vector with columns containing addition IDs

nr_children

name of columns with the number of peptides

Methods

Public methods

• ProteinAnnotation$new()

• ProteinAnnotation$annotate_decoys()

• ProteinAnnotation$annotate_contaminants()

• ProteinAnnotation$nr_clean()

• ProteinAnnotation$clean()

• ProteinAnnotation$clone()

---

Method new()

initialize

Usage

ProteinAnnotation$new(
  lfqdata,
  row_annot = NULL,
  description = NULL,
  ids = NULL,
  nr_children = "nr_peptides"
)

Arguments

lfqdata

data frame from setup_analysis

row_annot

data frame with row annotation. Must have columns matching config$table$hierarchy_keys_depth()

description

name of column with description

ids

names of columns with cleaned Ids

nr_children

column with the number of children

nr_peptides

additional peptides

---

Method annotate_decoys()

annotate rev sequences

Usage

ProteinAnnotation$annotate_decoys(pattern = "REV_")

Arguments

pattern

default "REV_"

---

Method annotate_contaminants()

annotate contaminants

Usage

ProteinAnnotation$annotate_contaminants(pattern = "^zz|^CON")

Arguments

pattern

default "^zz|^CON"

---

Method nr_clean()

get number of neither contaminants nor decoys

Usage

ProteinAnnotation$nr_clean(contaminants = TRUE, decoys = TRUE)

Arguments

contaminants

remove contaminants

decoys

remove decoys return number of cleans

---

Method clean()

remove REV and CON sequences

Usage

ProteinAnnotation$clean(contaminants = TRUE, decoys = TRUE)

Arguments

contaminants

remove contaminants

decoys

remove decoys

---

Method clone()

The objects of this class are cloneable with this method.

Usage

ProteinAnnotation$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

See Also

Other LFQData: LFQData, LFQDataAggregator, LFQDataPlotter, LFQDataStats, LFQDataSummariser, LFQDataToSummarizedExperiment(), LFQDataWriter

Examples

istar <-prolfqua::sim_lfq_data_peptide_config()
lfqdata <- LFQData$new(istar$data, istar$config)
pannot <- ProteinAnnotation$new( lfqdata )
pannot$annotate_decoys()
pannot$annotate_contaminants()
dd <- pannot$clean()
tmp <- lfqdata$get_subset(dd)
pannot$row_annot

wolski/prolfqua documentation built on May 12, 2024, 10:16 p.m.