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Question: deseq2 estimating size factors
1
gravatar for gv
22 months ago by
gv30
United States
gv30 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 22 months ago by Michael Love16k • written 22 months ago by gv30
3
gravatar for Michael Love
22 months ago by
Michael Love16k
United States
Michael Love16k 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 22 months ago by Michael Love16k

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 22 months ago by gv30
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 22 months ago • written 22 months ago by Michael Love16k
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 22 months ago • written 22 months ago by Michael Love16k
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