confirmColumnNames: Identify the Columns needed for Data Processing

In ksong4/NetPhorce: Phosphoproteomics Network Analysis (NetPhorce)

Identify the Columns needed for Data Processing

Description

The function selects the correct columns. Please note that the column name is case-sensitive.

Usage

confirmColumnNames(
  rawMaxQuant = rawMaxQuant,
  positionCol = positionCol,
  reverseCol = reverseCol,
  localizationProbCol = localizationProbCol,
  potentialContaminationCol = potentialContaminationCol,
  aminoAcidCol = aminoAcidCol,
  uniqueIDCol = uniqueID,
  seqWindowIDCol = seqWindowID,
  fastaIDCol = NULL
)

Arguments

rawMaxQuant	(Required). Loaded raw MaxQuant data
positionCol	(Required). List the column name with the phosphorylation position.
reverseCol	(Required). List the column with the reverse information.
localizationProbCol	(Required). List the column name with the localization probability.
potentialContaminationCol	(Required). List the column name with the contamination information.
aminoAcidCol	(Required). List the column name with the amino acid.
uniqueIDCol	(Required). List the column name with the protein for the peptides.
seqWindowIDCol	(Required). List the column name with the sequence window.
fastaIDCol	(Optional). List the column name with the FASTA header.

Value

A list of data.frames

Examples

## Not run: 
## Loading One Condition Data
data("oneConditionExample")
## Identify the Columns needed for Data Processing
identifiedCols <- confirmColumnNames(rawMaxQuant = oneConditionExample,
                                	    positionCol = "Position",
                                	    reverseCol = "Reverse",
                                     localizationProbCol = "Localization prob",
                                     potentialContaminationCol = "Potential contaminant",
                                     aminoAcidCol = "Amino acid",
                                	    uniqueIDCol = "Protein",
                                     seqWindowIDCol = "Sequence window",
                    	                fastaIDCol = "Fasta headers")

## End(Not run)

ksong4/NetPhorce documentation built on March 24, 2023, 12:51 p.m.