Description Usage Arguments Value Examples
Initialize and load input data into a NVTobject
1 2 | NVTinit(housekeeping_gene_list, expression_list_1, expression_list_2,
normalization_method, feat_length)
|
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 |
An NVTobject ready for normalization
1 2 3 4 5 6 7 8 9 | 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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.