TCGAanalyze_Filtering {TCGAbiolinks} | R Documentation

## Filtering mRNA transcripts and miRNA selecting a threshold.

### Description

TCGAanalyze_Filtering allows user to filter mRNA transcripts and miRNA, selecting a threshold. For istance returns all mRNA or miRNA with mean across all samples, higher than the threshold defined quantile mean across all samples.

### Usage

    TCGAanalyze_Filtering(tabDF, method, qnt.cut = 0.25, var.func = IQR,
      var.cutoff = 0.75, eta = 0.05, foldChange = 1)

### Arguments

`tabDF` | is a dataframe or numeric matrix, each row represents a gene, each column represents a sample come from TCGAPrepare
`method` | is method of filtering such as 'quantile', 'varFilter', 'filter1', 'filter2'
`qnt.cut` | is threshold selected as mean for filtering
`var.func` | is function used as the per-feature filtering statistic. See genefilter documentation
`var.cutoff` | is a numeric value. See genefilter documentation
`eta` | is a paramter for filter1. default eta = 0.05.
`foldChange` | is a paramter for filter2. default foldChange = 1.

### Value

A filtered dataframe or numeric matrix where each row represents a gene, each column represents a sample

### Examples

    dataNorm <- TCGAbiolinks::TCGAanalyze_Normalization(dataBRCA, geneInfo)
    dataNorm <- TCGAanalyze_Normalization(tabDF = dataBRCA,
    geneInfo = geneInfo,
    method = "geneLength")
    dataFilt <- TCGAanalyze_Filtering(tabDF = dataNorm, method = "quantile", qnt.cut = 0.25)

[Package TCGAbiolinks version 2.12.6 Index]