deseqAbs: Class a simple interface to deseq data

In perllb/deseqAbstraction: A set of functions to make DESeq pipes more smooth

Class a simple interface to deseq data

Description

Class a simple interface to deseq data

Usage

deseqAbs

Format

R6Class object.

Value

Object of R6Class to store Deseq data.

Fields

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

FPKMMean

list of data.frames: Mean and SD: mean and SD of FPKM

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)

FPKM

matrix with FPKM values for all genes

test

output from diffex analysis results(dds)

pos

position data for each gene

length

of each gene

Examples

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$makeFPKM()

perllb/deseqAbstraction documentation built on Oct. 31, 2023, 2:13 a.m.