Question: Problem annotating with COHCAP 1.16.0 in MacOsX
0
gravatar for IOM
2.9 years ago by
IOM20
Birmingham
IOM20 wrote:

Hi,

Thanks for reading. I am trying to replicate this pipeline (COHCAP: City of Hope CpG Island Analysis Pipeline,Charles Warden November 4, 2016) and I am finding some issues.

I have generated 3 .txt files: 
One for the **samples** (37 at all), with following structure
200053740020_R02C02    Group1
200053740019_R02C01    Group1
200053740019_R05C01    Group1
200053740019_R02C02    Group1
200053740019_R03C02    Group1
200053740095_R02C02    Group2
200053740095_R03C02    Group2
200053740034_R04C02    Group2
...
One for the **Beta** values, with following structure
    200053740034_R03C02    200053740134_R01C02...
cg13869341    0.807718263    0.811597173...
cg14008030    0.630174852    0.664826422...
cg12045430    0.24139956    0.303547345...
...
Another one with the **RNA-seq** intensities 
Gene Symbol    200053740034_R02C01    200053740034_R03C01
5S_rRNA    -0.894804008    -1.514165631
7SK    4.559935916    5.869538661
A1BG    -3.70215893    -0.777200037
A1BG-AS1    -2.117196429    -0.777200037
A1CF    -3.70215893    -1.514165631

When I run following line with 450k-UCSC annotation I get 0 as result
> beta.table = COHCAP.annotate(beta.file, project.name, project.folder,platform="450k-UCSC")
[1] 483835     38
[1] 0 5
[1]  0 42
and the table looks like this 
> beta.table
 [1] SiteID               Chr                  Loc                  Gene                
 [5] Island               X200053740034_R03C02 X200053740134_R01C02 X200053740134_R05C02
 [9] X200053740095_R01C01 X200053740095_R03C01 X200053740020_R03C02 X200053740019_R01C01
[13] X200053740006_R01C01 X200053740006_R04C01 X200053740006_R06C01 X200053740006_R02C02
[17] X200053740006_R03C02 X200053740006_R05C02 X200053740095_R02C02 X200053740095_R03C02
[21] X200053740034_R04C01 X200053740034_R04C02 X200053740134_R04C01 X200053740095_R06C01
[25] X200053740100_R04C01 X200053740100_R05C01 X200053740100_R03C02 X200053740020_R01C01
[29] X200053740020_R06C01 X200053740020_R01C02 X200053740020_R02C02 X200053740020_R05C02
[33] X200053740019_R02C01 X200053740019_R05C01 X200053740019_R02C02 X200053740019_R03C02
[37] X200053740006_R02C01 X200053740059_R01C01 X200053740059_R03C01 X200053740059_R01C02
[41] X200053740059_R02C02 X200053740059_R05C02
<0 rows> (or 0-length row.names)

When I run it with my annotation file I get something similar
> beta.table = COHCAP.annotate(beta.file, project.name, project.folder,platform="custom",annotation.file = "annotation.txt")
[1] 483835     38
[1] "Using custom island/gene annotations from : annotation.txt"
[1] 485512     33
[1]  0 33
[1]  0 70

And the table looks similar
> beta.table
 [1] chr                      pos                      strand                  
 [4] Name                     AddressA                 AddressB                
 [7] ProbeSeqA                ProbeSeqB                Type                    
[10] NextBase                 Color                    Probe_rs                
[13] Probe_maf                CpG_rs                   CpG_maf                 
[16] SBE_rs                   SBE_maf                  Islands_Name            
[19] Relation_to_Island       Forward_Sequence         SourceSeq               
[22] Random_Loci              Methyl27_Loci            UCSC_RefGene_Name       
[25] UCSC_RefGene_Accession   UCSC_RefGene_Group       Phantom                 
[28] DMR                      Enhancer                 HMM_Island              
[31] Regulatory_Feature_Name  Regulatory_Feature_Group DHS                     
[34] X200053740034_R03C02     X200053740134_R01C02     X200053740134_R05C02    
[37] X200053740095_R01C01     X200053740095_R03C01     X200053740020_R03C02    
[40] X200053740019_R01C01     X200053740006_R01C01     X200053740006_R04C01    
[43] X200053740006_R06C01     X200053740006_R02C02     X200053740006_R03C02    
[46] X200053740006_R05C02     X200053740095_R02C02     X200053740095_R03C02    
[49] X200053740034_R04C01     X200053740034_R04C02     X200053740134_R04C01    
[52] X200053740095_R06C01     X200053740100_R04C01     X200053740100_R05C01    
[55] X200053740100_R03C02     X200053740020_R01C01     X200053740020_R06C01    
[58] X200053740020_R01C02     X200053740020_R02C02     X200053740020_R05C02    
[61] X200053740019_R02C01     X200053740019_R05C01     X200053740019_R02C02    
[64] X200053740019_R03C02     X200053740006_R02C01     X200053740059_R01C01    
[67] X200053740059_R03C01     X200053740059_R01C02     X200053740059_R02C02    
[70] X200053740059_R05C02    
<0 rows> (or 0-length row.names)

Any idea of why this could be happening? It is the first time I am using COHCAP and I am probably missing something. Thanks very much for your time and attention and merry christmas!!

IOM

ADD COMMENTlink written 2.9 years ago by IOM20
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