runDoscheda: Wrapper Function to run the entire Doscheda pipeline

Description Usage Arguments Value See Also Examples

View source: R/runDoscheda.R

Description

A wrapper for the whole Doscheda pipeline, if users want to avoid using the separate steps.

Usage

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runDoscheda(dataFrame, dataChannels, accessionChannel, chansVal, repsVal,
  dataTypeStr, modelTypeStr, PDBool = TRUE, removePepsBool = NA,
  incPDofPDBool = FALSE, PDofPDname = NA, incGeneFileBool = FALSE,
  organismStr = "h.sapiens", sigmoidConc = NA, pearsonThrshVal = 0.4,
  uniquePeps = NA, sequenceChannel = NA, qualityChannel = NA,
  pdofpdChannel = NA, incGeneID = FALSE, geneIDFile = NA,
  normType = "loess")

Arguments

dataFrame

data.frame of the input data set

dataChannels

column names of dataFrame that correspond to data channels. These should be ordered in the format: rep1_concentration_0, ..., rep1_concentration_n, rep2_concentration_0, ...

accessionChannel

string that is the same as the column name for the protein accessions in dataFrame

chansVal

number of channels / concentrations in experiment

repsVal

number of replicates in experiment

dataTypeStr

string describing the data type of input data set. This can be 'LFC' for log fold-changes, 'FC' for fold-changes and 'intensity' for peptide intensities

modelTypeStr

string describing the type of model applied. This can be 'linear' for a linear model or 'sigmoid' for a sigmoidal model

PDBool

boolean value indicating if the input data is from Proteome Discoverer 2.1 or not

removePepsBool

boolean value indicating if peptide removal will take place. Only valid if input data is peptide intensities

incPDofPDBool

boolean value indicating if the input data contais a pull-down of pull-down colum

PDofPDname

string with the same name as colulmn containing pull-down of pull-down data. NA if this is not applicable

incGeneFileBool

boolean value indicating if the data requires a protein accession to gene ID conversion file

organismStr

string giving the name of organism. the options are: 'H.sapiens', 'D. melanogaster', 'C. elegans', 'R. norvegicus', 'M. musculus'. This is only needed if PDbool is FALSE

sigmoidConc

vector of numerical values for concentrations of channels in the case of a sigmoidal fit

pearsonThrshVal

numerial value between -1 and 1 which determines the cut-off used to discard peptides during peptide removal

uniquePeps

string that is the same as the column name for the number of unique peptides in dataFrame

sequenceChannel

string that is the same as the column name for the peptide sequences in dataFrame

qualityChannel

string that is the same as the column name for the peptide quality score in dataFrame

pdofpdChannel

string that is the same as the column name for the pull-down of pull-down data in dataFrame

incGeneID

boolean value indicating if a protein accession to gene ID file is supplied

geneIDFile

data.frame containing a protein accession to gene ID conversion file

normType

string indicating the type of normalisation that should take place ('loess', 'median', 'none')

Value

object of class ChemoProtSet

See Also

DoschedaSet

Examples

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channelNames <- c('Abundance..F1..126..Control..REP_1',
'Abundance..F1..127..Sample..REP_1',  'Abundance..F1..128..Sample..REP_1',
'Abundance..F1..129..Sample..REP_1',  'Abundance..F1..130..Sample..REP_1',
'Abundance..F1..131..Sample..REP_1',  'Abundance..F2..126..Control..REP_2',
'Abundance..F2..127..Sample..REP_2', 'Abundance..F2..128..Sample..REP_2',
'Abundance..F2..129..Sample..REP_2',  'Abundance..F2..130..Sample..REP_2',
'Abundance..F2..131..Sample..REP_2')

ex <- runDoscheda(dataFrame = doschedaData, dataChannels = channelNames,
chansVal = 6, repsVal = 2,dataTypeStr = 'intensity',
modelTypeStr = 'linear',PDBool = FALSE,removePepsBool = FALSE,
accessionChannel = 'Master.Protein.Accessions',
sequenceChannel = 'Sequence',qualityChannel = 'Qvality.PEP',
incPDofPDBool = FALSE, incGeneFileBool = FALSE,
 organismStr = 'H.sapiens', pearsonThrshVal = 0.4)

brunocontrino/DOSCHEDA documentation built on Sept. 15, 2020, 12:12 a.m.