[BioC] DEXSeq: building exon count set

[Alejandro Reyes]

Dear Vincenzo,

The function newExonCountSet will do the job.
Have a look into the pasilla vignette, it explains how to generate an 
ExonCountSet object both from the outputs of the python script or from 
basic R objects.

Best regards,
Alejandro

> Dear all,
> I am using DEXSeq to make splicing analysis on my data.
> But I have a problem with the function read.HTSeqCounts: in the countfiles
> argument, HTSeqCounts get in input a vector with the paths to exon count
> files, but I have(as in DESeq package) a data.frame like this(computed by
> my pipeline):
>
>> head(countTable)
>                         X498_A X479_D X480_D X509_B X524_A X515_A X496_B
> X508_C
> ENSMUSG00000000001:001    338    397    404    350    404    381    485
> 521
> ENSMUSG00000000001:002     47     48     55     26     40     39     35
> 41
> ENSMUSG00000000001:003     23     12     37     17     14     18     27
> 15
> ENSMUSG00000000001:004     17      9     14     18      8      9     27
> 15
> ENSMUSG00000000001:005     16     15     16      9     13     18     16
> 24
> ENSMUSG00000000001:006     18     14     11     20     12     22     20
> 24
>                         X517_D X478_D X497_A X533_D X487_B X516_D X531_B
> X513_D
> ENSMUSG00000000001:001    514    513    387    620    579    627    467
> 616
> ENSMUSG00000000001:002     48     65     31     65     58     75     39
> 85
> ENSMUSG00000000001:003     19     35     26     32     25     34     22
> 29
> ENSMUSG00000000001:004     19     23      4     18     23     25     13
> 24
> ENSMUSG00000000001:005     16     17     11     12     20     24      8
> 18
> ENSMUSG00000000001:006     26     26      9     22     24     24     19
> 25
>                         X507_A X505_C X506_C X525_C X514_A X546_C X547_C
> X488_B
> ENSMUSG00000000001:001    569    725    621    488    534    575    639
> 1037
> ENSMUSG00000000001:002     52     66     57     56     42     70     63
> 89
> ENSMUSG00000000001:003     30     40     33     26     19     24     27
> 62
> ENSMUSG00000000001:004     23     20     25     22     22     18     19
> 30
> ENSMUSG00000000001:005     22     19     18      7     20     19     21
> 35
> ENSMUSG00000000001:006     22     25     19     21     29     25     19
> 32
>
> My question is: Is there a way in which I can use function read.HTSeqCounts
> with my table as input?
> I used all DEXSeq python scripts to obtain my outputs.
>
> Thanks in advance.
> Regards,
>
> Vincenzo
>
> 	[[alternative HTML version deleted]]
>
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