User: jmKeith

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jmKeith0
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Posts by jmKeith

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Comment: C: Use csaw to build matrix for heatmap?
... Thank you very much for your help.  I understand now how to build the matrices, but I'm still a bit lost on how to filter for reads that fall within peaks.  Would you mind going through that part one more time? Very much appreciated, Julia ...
written 9 months ago by jmKeith0
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Use csaw to build matrix for heatmap?
... Hello, Can anyone help me understand how to use csaw to 1) filter my BAM file reads to retain only windows within MACS called peaks, 2) then count the number of reads in 100bp bins within a 5kbp region around each peak?   I have my BAM reads file, my BED peaks file and then an additional BED file ...
chipseq edger csaw written 9 months ago by jmKeith0 • updated 9 months ago by Aaron Lun17k
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Answer: A: ChIPpeakAnno-annotation of peaklist with gene names, creating heat maps
... Hello again, First, thank you very very much for the assistance and putting up with me.   I haven't had any luck in annotating my "peaklist" nor in the "peaksInMergedPeaks" lists.  I have also gone through the user's guide and the problem that I see is that both objects are of list class and the a ...
written 11 months ago by jmKeith0
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ChIPpeakAnno-annotation of peaklist with gene names, creating heat maps
... Hello,  I apologise for all the questions, but I have two more!   1) Is there a way to get gene names on the "peaklist" object obtained from the findOverlapOfPeaks function? I'm able to get the peaklist but it's just a very long list of all the peaks per comparison (ie: given peaksA, peaksB, peaks ...
annotation chippeakanno overlappingpeaks written 11 months ago by jmKeith0 • updated 11 months ago by Ou, Jianhong1000
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Comment: C: ChIPpeakAnno-problem exporting data due to "arguments imply differing number of
... Thanks very much! ...
written 11 months ago by jmKeith0
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Comment: C: ChIPpeakAnno-problem exporting data due to "arguments imply differing number of
... I think I've got it--thank you for pointing out the fact that I was trying to write out a list, without thinking about the fact that it's a list!   This is the script that I've used- >lapply(annotated.overlaplist, function(x) write.table( data.frame(x), 'annotated.overlaplist.txt'  , append= T, ...
written 11 months ago by jmKeith0
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Answer: A: ChIPpeakAnno-problem exporting data due to "arguments imply differing number of
... In contrast, my annotated.overlaplist list object is the full list at 7MB --the first few lines are below.   > annotated.overlaplist $`d3.k4m1.TGR///d3.k27Ac.TGR`                                                        peaks1     seqnames     start d3.k27Ac.TGR__X00003_d3.k4m1.TGR__X00002 d3.k27A ...
written 11 months ago by jmKeith0
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Answer: A: ChIPpeakAnno-problem exporting data due to "arguments imply differing number of
... Hi, Again, thank you for your help.  I've tried the script that you sent, but what I get is an almost entirely blank object.   > overlapping <- mapply(write.table, annotated.overlaplist, gsub("\\/+", ".", paste0("annotated.overlaplist_", names(annotated.overlaplist), ".txt"))) > overlappi ...
written 11 months ago by jmKeith0
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ChIPpeakAnno-problem exporting data due to "arguments imply differing number of rows"
... Hello, I have been doing a three way analysis of ChIP-Seq data (histone modifications) using ChIPpeakAnno and I am having difficulty exporting my data.  I am able to find overlapping peaks for my three peak files, but am unable to write out the file using any "write" function that I have tried due ...
chippeakanno written 11 months ago by jmKeith0 • updated 11 months ago by Julie Zhu3.8k
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Answer: A: How to fix ChIPPeakAnno error in adding gene names to annotated peaks?
... Thanks!  I saw that I had an error in that I was trying to use both mart and data arguments at the same time.  An accident of playing around with various parameters.  Many thanks for your help! ...
written 11 months ago by jmKeith0

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