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
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
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