significantVals {TimiRGeN} | R Documentation

## 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")

[Package TimiRGeN version 1.4.0 Index]