TCGAanalyze_Filtering: Filtering mRNA transcripts and miRNA selecting a threshold.

In TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

Description

TCGAanalyze_Filtering allows user to filter mRNA transcripts and miRNA, 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 parameter for filter1. default eta = 0.05.
foldChange	is a parameter 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)

TCGAbiolinks documentation built on Nov. 8, 2020, 5:37 p.m.