User: jmKeith

jmKeith0
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Posts by jmKeith

<prev • 11 results • page 1 of 2 • next >
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... 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 22 months ago by jmKeith0
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... 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 ...
written 22 months ago by jmKeith0 • updated 22 months ago by Aaron Lun21k
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... 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 23 months ago by jmKeith0
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... 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 ...
written 24 months ago by jmKeith0 • updated 23 months ago by Ou, Jianhong1.1k
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... Thanks very much! ...
written 2.0 years ago by jmKeith0
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... 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 2.0 years ago by jmKeith0
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... 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 2.0 years ago by jmKeith0
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... 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 2.0 years ago by jmKeith0
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... 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 ...
written 2.0 years ago by jmKeith0 • updated 2.0 years ago by Julie Zhu3.9k
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... 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 2.0 years ago by jmKeith0

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