cummeRbund get isoforms

paolo.kunder · 02-16-2012, 03:31 AM

Hi,
I am facing some problems with cummeRbund R package:

library(cummeRbund)
cuff <- readCufflinks()

#get the top 5 diff expr isoforms
iso.diff <- diffData(isoforms(cuff))
iso.diff.top <- iso.diff[order(iso.diff$q_value),][1:5,]

iso.diff.top

isoform_id sample_1 sample_2 status value_1 value_2 ln_fold_change
20524 TCONS_00020591 controlli casi OK 13.0221 1.18723 -3.45528e+00
39253 TCONS_00039380 controlli casi OK 0.0000 7.12244 1.79769e+308
75370 TCONS_00075672 controlli casi OK 31.1991 4.17233 -2.90258e+00
75504 TCONS_00075806 controlli casi OK 18.1982 2.19050 -3.05446e+00
75485 TCONS_00075787 controlli casi OK 13.1554 1.39641 -3.23587e+00

myIsoIds <- iso.diff.top$isoform_id
myIsoIds
TCONS_00039380.....etc

how I do extract Isoforms values and plot for instance an expression bar plot?

how I interact with Isoforms database and extract isoforms values like I do with genes values (myGenes <- getGenes(cuff, myGeneIds))

Any suggestions will be appreciated,

CIAO!
Paolo

lgoff · 02-16-2012, 08:36 AM

Hi Paolo,
This is something that I am working to build into the next public release of cummeRbund. I recognize the need for a 'getFeatures()' method similar to getGenes() but not tied to the gene-based hierarchy.

In the meantime, you should be able to take the results of the call to fpkm(isoforms(cuff)), apply your filtering, and then create a ggplot2 object using that data directly. Everything you need to plot expression values should be output by this method.

Let me know if I can help with anything else.

Cheers,
Loyal

vyellapa · 02-21-2012, 06:47 PM

While installling cummeRbund 1.0.0 on R 2.14 , Im getting a "reshape2" package not found. While trying to manually install "respahe2", I have dependency errors to install packages "stringr", "evaluate" and "testhat". Im not sure how to install the dependencies as there is a deadlock while installing packages. For example, when I try to install "stringr" the error is that "evaluate" dependency is not install and vice-versa. Is there an easy way to install reshape2 with all its dependencies?

lgoff · 02-21-2012, 09:16 PM

You can install reshape2 and all of its dependencies by starting an R session and typing:

Code:

install.packages('reshape2')

Cheers,
Loyal

beta.gal · 06-03-2012, 06:45 PM

Hi,

Now that the newer beta version of cummeRbund is out, I was wondering if the getFeatures, or something like it, had been introduced? I have not been able to detect anything like this from the manual.

Regards,
Paula

lgoff · 06-04-2012, 05:18 AM

Quote:

Originally Posted by beta.gal

Hi,

Now that the newer beta version of cummeRbund is out, I was wondering if the getFeatures, or something like it, had been introduced? I have not been able to detect anything like this from the manual.

Regards,
Paula

Hi Paula,
A getFeatures() method has indeed been introduced ( I think it was introduced in v.1.99.2) it works with the same type of arguments as getGenes(), but returns a cuffFeatureSet instead of retrieving all gene information. You can find details by calling

Code:

> ?getFeatures()

Cheers,
Loyal

mbjohnson · 04-23-2014, 08:59 AM

Hi Loyal -
I successfully added additional annotations at the gene and isoform levels using addFeatures(). However, these extra annotations were not included in the output of getFeatures() using either level="genes" or level="isoforms". The extra annotations were there using getGenes() but I'm mostly interested in getting only the significant isoforms (with all my added annotations). So I was happy to find the getFeatures() function but it looks like this may be a bug in it.
Thanks!
Matt

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02-16-2012, 03:31 AM	#1
paolo.kunder Member Location: Milano, Italy Join Date: Aug 2011 Posts: 93	cummeRbund get isoforms Hi, I am facing some problems with cummeRbund R package: library(cummeRbund) cuff <- readCufflinks() #get the top 5 diff expr isoforms iso.diff <- diffData(isoforms(cuff)) iso.diff.top <- iso.diff[order(iso.diff$q_value),][1:5,] iso.diff.top isoform_id sample_1 sample_2 status value_1 value_2 ln_fold_change 20524 TCONS_00020591 controlli casi OK 13.0221 1.18723 -3.45528e+00 39253 TCONS_00039380 controlli casi OK 0.0000 7.12244 1.79769e+308 75370 TCONS_00075672 controlli casi OK 31.1991 4.17233 -2.90258e+00 75504 TCONS_00075806 controlli casi OK 18.1982 2.19050 -3.05446e+00 75485 TCONS_00075787 controlli casi OK 13.1554 1.39641 -3.23587e+00 myIsoIds <- iso.diff.top$isoform_id myIsoIds TCONS_00039380.....etc how I do extract Isoforms values and plot for instance an expression bar plot? how I interact with Isoforms database and extract isoforms values like I do with genes values (myGenes <- getGenes(cuff, myGeneIds)) Any suggestions will be appreciated, CIAO! Paolo

02-21-2012, 06:47 PM	#3
vyellapa Member Location: phoenix Join Date: Oct 2011 Posts: 59	cummeRbund Installation While installling cummeRbund 1.0.0 on R 2.14 , Im getting a "reshape2" package not found. While trying to manually install "respahe2", I have dependency errors to install packages "stringr", "evaluate" and "testhat". Im not sure how to install the dependencies as there is a deadlock while installing packages. For example, when I try to install "stringr" the error is that "evaluate" dependency is not install and vice-versa. Is there an easy way to install reshape2 with all its dependencies?

02-21-2012, 09:16 PM	#4
lgoff Member Location: Cambridge, MA Join Date: Feb 2008 Posts: 82	You can install reshape2 and all of its dependencies by starting an R session and typing: Code: install.packages('reshape2') Cheers, Loyal

02-16-2012, 08:36 AM	#2
lgoff Member Location: Cambridge, MA Join Date: Feb 2008 Posts: 82	Hi Paolo, This is something that I am working to build into the next public release of cummeRbund. I recognize the need for a 'getFeatures()' method similar to getGenes() but not tied to the gene-based hierarchy. In the meantime, you should be able to take the results of the call to fpkm(isoforms(cuff)), apply your filtering, and then create a ggplot2 object using that data directly. Everything you need to plot expression values should be output by this method. Let me know if I can help with anything else. Cheers, Loyal

06-03-2012, 06:45 PM	#5
beta.gal Junior Member Location: Australia Join Date: Jun 2012 Posts: 1	Hi, Now that the newer beta version of cummeRbund is out, I was wondering if the getFeatures, or something like it, had been introduced? I have not been able to detect anything like this from the manual. Regards, Paula

04-23-2014, 08:59 AM	#7
mbjohnson Member Location: Boston, MA Join Date: Apr 2009 Posts: 15	Hi Loyal - I successfully added additional annotations at the gene and isoform levels using addFeatures(). However, these extra annotations were not included in the output of getFeatures() using either level="genes" or level="isoforms". The extra annotations were there using getGenes() but I'm mostly interested in getting only the significant isoforms (with all my added annotations). So I was happy to find the getFeatures() function but it looks like this may be a bug in it. Thanks! Matt