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Question: deseq2 estimating size factors
1
gravatar for gv
2.4 years ago by
gv40
United States
gv40 wrote:

Hi Everyone,

I am trying to run DESeq2 package in R. After running the package I have few questions. I will start with this.

baseMean : It is defines as average of the normalized count values, dividing by size factors, taken over all samples in the DESeqDataSet

After this step of the analysis,

ddsMat <- DESeqDataSetFromMatrix(count, colData, design=~condition

I ran

ddsMat <- DESeq(ddsMat)

In the above calculation I see estimating size factors

I want to know how I can get estimating size factors. What I want to do is to confirm the value of baseMean generated in the table for a particular gene.

 

How can I do this?

Thanks

Regards

Varun

 

ADD COMMENTlink modified 2.4 years ago by Michael Love19k • written 2.4 years ago by gv40
3
gravatar for Michael Love
2.4 years ago by
Michael Love19k
United States
Michael Love19k wrote:

There are a couple of approaches to finding information about a Bioconductor package. You can type:

vignette("DESeq2")

if you search the vignette for "size factors", one of the hits is in a section called "Access to all calculated values".

You can also browse all the DESeq2 manual pages by typing:

help(package="DESeq2", help_type="html")

If you search this page you will find some topics on size factors, including how to access the estimated size factors.

ADD COMMENTlink written 2.4 years ago by Michael Love19k

Hi Michael

Thanks for your reply. I found what i was looking for. Also how can i know which functions can be applied on CLASS DESeqDataSet? For example estimateSizefactors(dds), what else??

Thanks

ADD REPLYlink written 2.4 years ago by gv40
1

The complete list of methods is:

methods(class=class(dds))

But this includes *everything* that works on this object, including all the methods from the classes DESeqDataSet inherits, and you probably just want the package specific functions.

I wrote some messy code which gets this:

intersect(sapply(strsplit(as.character(methods(class="DESeqDataSet")), ","), `[`, 1), ls("package:DESeq2"))

This is an intersection between the character string of the methods names...

as.character(methods(class="DESeqDataSet")

...(after removing the class name parts of the signature) and the functions in the DESeq2 package...

ls("package:DESeq2")

Maybe there is a better way.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Michael Love19k
1

Martin pointed me to: 

showMethods(classes="DESeqDataSet", where=getNamespace("DESeq2"))

And you can get a short list with this messy code:

sub("Function: (.*) \\(package .*\\)","\\1",grep("Function",showMethods(classes="DESeqDataSet", where=getNamespace("DESeq2"), printTo=FALSE), value=TRUE))

 

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Michael Love19k
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