TCGAanalyze_Filtering {TCGAbiolinks} | R Documentation |
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.
TCGAanalyze_Filtering(tabDF, method, qnt.cut = 0.25, var.func = IQR, var.cutoff = 0.75, eta = 0.05, foldChange = 1)
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. |
A filtered dataframe or numeric matrix where each row represents a gene, each column represents a sample
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)