significantVals: significantVals

In Krutik6/TimiRGeN: Time sensitive microRNA-mRNA integration, analysis and network generation tool

significantVals

Description

Filters out genes in each nested dataframe which are not deemed significantly differentially expressed. Each sample will be filtered independently.

Usage

significantVals(MAE, method = '', geneList, maxVal, stringVal = '')

Arguments

MAE	MultiAssayExperiment to store the output of significantVals. It is recommended to use the MAE used in the genesList.
method	Either "c" or "s", respectively for combined or separated analysis.
geneList	A list of nested dataframes if "c" analysis is used or a list of lists of nested dataframes if "s" is used. This will be the output from them genesList function. The resulting list will be found as metadata, in the MAE used in the genesList function.
maxVal	Numeric value which represents the maximum cut off value for significance e.g. 0.05.
stringVal	Character. Common DE result type which is found in all nested dataframes. This will be used for filtration e.g. pval, adjPval or qval. Make sure the spelling matches the colnames for each sample.

Value

A list of dataframes with only significantly differentially expressed genes. Output will be stored as metadata within the input MAE.

Examples

miR <- mm_miR[1:50,]

mRNA <- mm_mRNA[1:100,]

Data <- startObject(miR = mm_miR, mRNA = mm_mRNA)

Data <- combineGenes(MAE = Data, miR_data = assay(Data, 1),
                     mRNA_data = assay(Data, 2))

Data <- genesList(MAE = Data, method = 'c', genetic_data = assay(Data, 3),
                  timeString = 'D')

Data <- significantVals(MAE = Data, method = 'c',
                        geneList = metadata(Data)[[1]],
                        maxVal = 0.05, stringVal = "adjPVal")

Krutik6/TimiRGeN documentation built on Jan. 27, 2024, 7:46 p.m.