## User: jmKeith

jmKeith0
Reputation:
0
Status:
New User
Last seen:
4 months ago
Joined:
2 years, 8 months ago
Email:
j**********@ndm.ox.ac.uk

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

#### Posts by jmKeith

<prev • 12 results • page 1 of 2 • next >
0
119
views
0
... Hi, I'm having an issue with the ComplexHeatmap package. Specifically, when I try to create the heatmap image, R returns the parameters of the map but not the actual image. No errors are reported however. When I use the regular base "heatmap" function, I get an image just fine. This is what is d ...
written 4 months ago by jmKeith0 • updated 4 months ago by James W. MacDonald50k
1
603
views
1
... 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 2.6 years ago by jmKeith0
1
603
views
1
... 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 2.6 years ago by jmKeith0 • updated 2.6 years ago by Aaron Lun24k
3
566
views
3
... 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 2.7 years ago by jmKeith0
3
566
views
3
... 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 2.7 years ago by jmKeith0 • updated 2.7 years ago by Ou, Jianhong1.1k
4
1.2k
views
4
... Thanks very much! ...
written 2.7 years ago by jmKeith0
4
1.2k
views
4
... 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 2.7 years ago by jmKeith0
4
1.2k
views
4
... 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 2.7 years ago by jmKeith0
4
1.2k
views
4
... 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 2.7 years ago by jmKeith0
4
1.2k
views
4
... 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 2.7 years ago by jmKeith0 • updated 2.7 years ago by Julie Zhu4.0k

#### Latest awards to jmKeith

Popular Question 2.5 years ago, created a question with more than 1,000 views. For ChIPpeakAnno-problem exporting data due to "arguments imply differing number of rows"

Content
Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.