[BioC] chippeakanno

[Zhu, Julie]

Hi Juerg,

Please see my comments below! Thanks!

Best regards,

Julie


On 6/15/10 11:25 AM, "Straubhaar, Juerg" <Juerg.Straubhaar at umassmed.edu>
wrote:

> Hi Julie,
> 
> I have a question on the output of annotatePeakInBatch (package chippeakanno):
> 
> I have this output:
> 
>        space     start       end        width names
> peak                            strand feature
> start_position end_position insideFeature            distancetoFeature
> shortestDistance 
> 
> 4     1 183100342 183100651   310 MACS_peak_1003 ENSMUSG00000062169
> MACS_peak_1003      1 ENSMUSG00000062169      183081062    18309912
> downstream             19280                     1217
> 
> 
> fromOverlappingOrNearest
> 
> NearestStart
> 
> 
> My interpretation::
> 
> insideFeature: downstream: the TSS is downstream of the peak start, ok
> 

The peak is downstream of the TSS

> distancetoFeature: 19280, the TSS starts 19280nt downstream from start of peak
> (start column), ok
> 

The distance from the peak start to TSS

> shortestDistance: 1217, distance to where? fromOverlappingOrNearest says
> NearestStart, but nearest start is 19280nt ?
> 

Minimum of (abs(peak start - feature start), abs(peak start - feature end),
abs(peak end - feature start), abs(peak end - feature end)) where abs is
short for absolute value. Please note that TSS is the feature start when the
feature is on plus strand and the feature end when the feature is on minus
strand.

> Kind regards,
> Juerg