Entering edit mode
Alec,
Thank you very much for your feedback and kind words!
ChIPpeakAnno does not keep the score in the annotated output. However,
you
could use add score to the annotated data. Here is the psudo code.
AnnotatedPeak = as.data.frame(annotatePeakInBatch(...))
Data.withScore = read.table(yourBedfile, sep="\t", header=FALSE)
Colnames(Data.withScore)[1:5] =c("chrom", "start", "end", "name",
"score")
AnnotatedPeak.withScore = merge(AnnotatedPeak, Data.withScore[,1:5],
by.x=c("space", "start", "end"), by.y= c("chrom", "start", "end"),
all=TRUE)
Hope this is what you are looking for.
Best regards,
Julie
On 10/9/13 6:03 PM, "Alec W. Uebersohn" <alec.w.uebersohn at="" lawrence.edu="">
wrote:
> Hello!
>
> I am currently sitting on a mountain of ChIP-seq data and I first
would like
> to say that ChIPpeakAnno has been of great help to me and my PI, who
are
> taking this project on alone, so thank you very much for you and
your team's
> contribution to biology and bioinformatics! I have a question
regarding
> ChIPpeakAnno's use of BED scores, or what is essentially the
averaged ChIP
> counts for our peaks. When performing the BED2RangedData function,
do these
> numbers carry forward into the ranged data? Is there a way to make
them do
> so, and also carry forward into the annotation data? I am happy
with the job
> this package does in annotating my peaks, but I also would like the
final
> table of data to contain the BED score/ChIP counts for each
annotated peak so
> that I can rank genes by their level of enrichment in our ChIP-seq
experiment.
> Is there a way for ChIPpeakAnno to do this? My only other idea was
to
> annotate with, for example, the select="first" argument to obtain a
list of
> single annotations for each peak (so each peak appears only once in
the
> annotation table) and then sort that table in the same way my BED
file is
> sorted so that I can copy and paste the BED file's "score" column
into the
> annotation table and then assume that it aligned properly.
>
> Thank you so much for any help or advice you can offer!
>
>
> Alec W. Uebersohn
> Research Technician, Dickson Lab
> Lawrence University '13
> Cell: (262) 443-4949