User: Chris Seidel

gravatar for Chris Seidel
Chris Seidel50
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50
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United States
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5 months, 2 weeks ago
Joined:
4 years, 7 months ago
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Posts by Chris Seidel

<prev • 10 results • page 1 of 1 • next >
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Comment: C: New Version of R cannot coerce "GRanges" to "RangesList"
... Yes, RangesList is a thing. The Views() function could take an RLE coverage object and a RangesList, and return coverages on the ranges. I have a bunch of code to find coverage on regions that's all broken now because I can't convert GRanges to RangesList. Like hicklingmeb, I'm looking for whatever ...
written 10 months ago by Chris Seidel50
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Answer: A: How to Find Common Dysregulated Genes in Two or More Sets of Microarray Data?
... You could make a contingency table and use a Fisher Exact test, or you could use the hypergeometric distribution (see ?phyper in R). Given a universe of genes in two experiments, if you identify a set of genes in experiment 1, and another set of genes in experiment 2, these can help you evaluate the ...
written 4.1 years ago by Chris Seidel50
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Answer: A: Assessing RNA-Seq sample replicates
... As Gordon says, MDS plots are great for examining replicate relationships. Other simple things to do would be to examine correlation among your replicates/samples. For instance, given a table of counts: heatmap(cor(counts), scale="none") Or a heat map with a legend: library(gplots) heatmap.2(co ...
written 4.2 years ago by Chris Seidel50
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Answer: A: summing integer RLE
... Your Rle object has the same name for more than one element. Since this doesn't provide specificity, if you want to sum a particular element, you might refer to it specifically (i.e. not by name): sum(RleListexample[[1]]) Or if you want to sum all the elements named "seq1" you might create a bool ...
written 4.2 years ago by Chris Seidel50
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Comment: C: makeTranscriptDbFromBiomart failure from Data Anomaly
... Thanks very much. I'll update. And next time I'll check versions first. ...
written 4.2 years ago by Chris Seidel50
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Comment: C: makeTranscriptDbFromBiomart failure from Data Anomaly
... Thanks for the investigation, and the explanation! ...
written 4.2 years ago by Chris Seidel50
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makeTranscriptDbFromBiomart failure from Data Anomaly
... I get an error while trying to create a TranscriptDb object using the makeTranscriptDbFromBiomart() function from the GenomicFeatures library. The error message is below (truncated to show just the first transcript). The last time I ran this code was with Ensembl74, whereas today it is failing with ...
biomart genomicfeatures written 4.2 years ago by Chris Seidel50 • updated 4.2 years ago by Hervé Pagès ♦♦ 13k
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viewApply drops feature names; transfer names between lists
... Hello, I have a set of gene features on which I calculated coverage using Views: # get coverage for a tss RangesList tss.cov <- mapply(Views,mycov,tss.RL) # convert from list to SimpleRleViewsList tss.cov <- RleViewsList(tss.cov) # summarize values using mean or median tss.avg &l ...
coverage convert written 5.1 years ago by Chris Seidel50
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Answer: A: how to operate on a DNAStringSet object
... Hello Steve and Herve, Thanks very much! Holy cow! Randomize a string set with endoapply(xx, sample). This is the essence of my love/hate relationship with programming. I've spent my share of quality time with the IRanges vignette, and I still would have never thought of that 21 character one- line ...
written 6.2 years ago by Chris Seidel50
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how to operate on a DNAStringSet object
... I can't figure out how to operate on a DNAStringSet object, and get a DNAStringSet object back. I have a DNAStringSet object for which I'd like to randomize the order of nucleotides in the sequences. Here is a simple example: # function to randomly re-order a string randomizeSeq <- function(mys ...
bsgenome written 6.2 years ago by Chris Seidel50

Latest awards to Chris Seidel

Popular Question 10 months ago, created a question with more than 1,000 views. For makeTranscriptDbFromBiomart failure from Data Anomaly
Popular Question 4.1 years ago, created a question with more than 1,000 views. For how to operate on a DNAStringSet object

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