normalyzer: NormalyzerDE pipeline entry point

Description Usage Arguments Details Value Examples

View source: R/NormalyzerDE.R

Description

This function is the main execution point for the normalization part of the NormalyzerDE analysis pipeline. When executed it performs the following steps:

Usage

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normalyzer(jobName, designPath = NULL, dataPath = NULL,
  experimentObj = NULL, outputDir = ".", forceAllMethods = FALSE,
  omitLowAbundSamples = FALSE, sampleAbundThres = 5,
  tinyRunThres = 50, requireReplicates = TRUE,
  normalizeRetentionTime = TRUE, plotRows = 3, plotCols = 4,
  zeroToNA = FALSE, sampleColName = "sample", groupColName = "group",
  inputFormat = "default", skipAnalysis = FALSE, quiet = FALSE,
  noLogTransform = FALSE, rtStepSizeMinutes = 1,
  rtWindowMinCount = 100, rtWindowShifts = 1,
  rtWindowMergeMethod = "mean")

Arguments

jobName

Give the current run a name.

designPath

Path to file containing design matrix.

dataPath

Specify an output directory for generated files. Defaults to current working directory.

experimentObj

SummarizedExperiment object, can be provided as input as alternative to 'designPath' and 'dataPath'

outputDir

Directory where results folder is created.

forceAllMethods

Debugging function. Run all normalizations even if they aren't in the recommended range of number of values

omitLowAbundSamples

Automatically remove samples with fewer non-NA values compared to threshold given by sampleAbundThres. Will otherwise stop with error message if such sample is encountered.

sampleAbundThres

Threshold for omitting low-abundant samples. Is by default set to 15.

tinyRunThres

If total number of features is less than this, a limited run is performed.

requireReplicates

Require multiple samples per condition to pass input validation.

normalizeRetentionTime

Perform normalizations over retention time.

plotRows

Number of plot-rows in output documentation.

plotCols

Number of plot-columns in output documentation.

zeroToNA

Convert zero values to NA.

sampleColName

Column name in design matrix containing sample IDs.

groupColName

Column name in design matrix containing condition IDs.

inputFormat

Type of input format.

skipAnalysis

Only perform normalization steps.

quiet

Omit status messages printed during run.

noLogTransform

Don't log-transform the input.

rtStepSizeMinutes

Retention time normalization window size.

rtWindowMinCount

Minimum number of datapoints in each retention-time segment.

rtWindowShifts

Number of layered retention time normalized windows.

rtWindowMergeMethod

Merge approach for layered retention time windows.

Details

1: Loads the data matrix containing expression values and optional annotations, as well as the design matrix containing the experimental setup 2: Performs input data verification to validate that the data is in correct format. This step captures many common formatting errors. It returns an instance of the NormalyzerDataset class representing the unprocessed data. 3: Calculate a range of normalizations for the dataset. The result is provided as a NormalyzerResults object containing the resulting data matrices from each normalization. 4: Analyze the normalizations and generate performance measures for each of the normalized datasets. This result is provided as a NormalyzerEvaluationResults object. 5: Output the matrices containing the normalized datasets to files. 6: Generate visualizations overviewing the performance measures and write them to a PDF report.

Value

None

Examples

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## Not run: 
data_path <- system.file(package="NormalyzerDE", "extdata", "tiny_data.tsv")
design_path <- system.file(package="NormalyzerDE", "extdata", "tiny_design.tsv")
out_dir <- tempdir()
normalyzer(
    jobName="my_jobname", 
    designPath=design_path, 
    dataPath=data_path, 
    outputDir=out_dir)
normalyzer(
    "my_jobname", 
    designMatrix="design.tsv", 
    "data.tsv", 
    outputDir="path/to/output", 
    normalizeRetentionTime=TRUE, 
    retentionTimeWindow=2)
normalyzer(
    "my_jobname", 
    designMatrix="design.tsv", 
    "data.tsv", 
    outputDir="path/to/output", 
    inputFormat="maxquantprot")

## End(Not run)

NormalyzerDE documentation built on Nov. 8, 2020, 8:22 p.m.