NVTinit: Initialize and load input data into a NVTobject

Description Usage Arguments Value Examples

View source: R/NVT-init.R

Description

Initialize and load input data into a NVTobject

Usage

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NVTinit(housekeeping_gene_list, expression_list_1, expression_list_2,
  normalization_method, feat_length)

Arguments

housekeeping_gene_list

A list of housekeeping-genes

expression_list_1

The first data frame of expression values per gene

expression_list_2

Second data frame of expression values per gene

normalization_method

The normalization method to use [N,TC,Med,TMM,UQ,UQ2,Q,RPKM,RPM,DEQ,TPM,G] N = No normalization, TC = Total count normalization, Med = Median normalization, TMM = Trimmed Mean of M-values normalization, UQ = Upper Quartile normalization , UQ2 = Upper Quartile normalization (from NOISeq), Q = Quantile normalization, RPKM = Reads Per Kilobase per Million mapped reads normalization, RPM = Reads per Million mapped reads normalization, DEQ = relative log expression method included in the DESeq package, TPM = transcripts per million normalization, G = use the provided genes to normalize

feat_length

A data frame of length per gene/exon

Value

An NVTobject ready for normalization

Examples

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library("NVT")
data(myexp1)
data(myexp2)
data(mylen)
mylist1<-c("ENSG00000111640","ENSG00000163631","ENSG00000075624","ENSG00000172053",
"ENSG00000170950","ENSG00000165704","ENSG00000196839","ENSG00000168938","ENSG00000177700")

mynvt <- NVTinit(mylist1,myexp1,myexp2,"N")
mynvt2 <- NVTinit(mylist1,myexp1,myexp2,"RPKM",mylen)

NexusX/NVT documentation built on June 25, 2021, 11:58 p.m.