deseqTE | R Documentation |
Class a simple interface to deseq with transposons - inherits from deseqAbstraction
deseqTE
R6Class
object.
Object of R6Class
to store Deseq data.
name
the name of the experiment
filename
the name of the raw featurecount output
rawfile
the raw featurecount file
rawCounts
the count matrix (removing position and length info column 1-6) with ID rownames
baseMean
list of data.frames: Mean and SD: mean and SD of normalized count data
rpkmMean
list of data.frames: Mean and SD: mean and SD of RPKM
geneID
geneIDs
colData
a data.frame with condition information
sampleNames
a vector given by user to provide suitable sampleNames to replace filenames from featureCounts
VST
the output from varianceStabilizingTransformation(dds)
deseq
the output from DESeq(dds)
rpkm
matrix with rpkm values for all genes
test
output from diffex analysis results(dds)
pos
position data for each gene
length
of each gene
dnmt <- deseqAbs$new("DNMT1KO",fc.file)
dnmt$filename
head(dnmt$rawfile)
head(dnmt$pos)
head(dnmt$length)
head(dnmt$rawCounts)
## sampleNames
dnmt$sampleNames <- colnames(dnmt$rawCounts)
## define coldata conditions
dnmt$colData <- data.frame(condition=c(rep("CTR",3),rep("KO",3)))
dnmt$makeDESeq()
dnmt$deseq
dnmt$makeDiffex()
dnmt$test
dnmt$makeVST()
dnmt$makeRPKM()
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