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Question: deseq2 estimating size factors
1
2.2 years 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

modified 2.2 years ago by Michael Love18k • written 2.2 years ago by gv30
3
2.2 years ago by
Michael Love18k
United States
Michael Love18k 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.

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

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.

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))