TCGAbiolinks (version 1.2.5)

TCGAanalyze_Filtering: 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)