miRNA_assessQualityThreshold {MiRNAQCD}

Assessment of quality threshold values.

Description

This function assesses a set of quality threshold values (standard deviations), one for each miRNA, out of a dataset.

Usage

miRNA_assessQualityThreshold(
  inputDataset,
  significanceLevel = 0.05,
  saveOutputFile = FALSE,
  outputFileName = "",
  sep = "\t"
)

Arguments

inputDataset

Dataset (data frame) to be used for the assessment. The data frame must comply with the output format of the preprocessing function (miRNA_expressionPreprocessing), thus containing the columns 'Subject', 'miRNA', 'Mean', 'StdDev', 'SampleSize' and possibly 'Class'. Any other column is ignored, and any missing column forbids execution.

significanceLevel

Significance level to be used for the assessment (must be greater than zero and less than one). Default is 0.05 (i.e. 5 percent).

saveOutputFile

Boolean option setting whether results are written to file (TRUE) or not (FALSE). Default is FALSE.

outputFileName

Name of the output file where the quality threshold values are to be stored. If not assigned, a filename is automatically generated.

sep

Field separator character for the output files; the default is tabulation.

Value

A data frame of quality threshold values, containing the columns 'miRNA' and 'QualityThreshold'.

Please refer to the user manual installed in "/path-to-library/MiRNAQCD/doc/manual.pdf" for detailed function documentation. The path "/path-to-library" can be shown from R by calling ".libPaths()"

Examples

requiredFile = paste(system.file(package="MiRNAQCD"),
		"/extdata/test_dataset_alpha_prep.dat", sep='')
myDataFrame <- read.table(file=requiredFile, header=TRUE)
qt <- miRNA_assessQualityThreshold(myDataFrame, significanceLevel=0.05)