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Results tagged with r
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user 29
Please supplement your question with a minimal reproducible example. Use dput() for data and specify all non-base packages with library calls. For statistical questions please use http://stats.stackexchange.com.
6
votes
Accepted
Count genomic ranges
GenomicRanges::countOverlaps seems to be what you’re after:
position_range = GRanges(position$chrom, IRanges(position, position, width = 1))
ranges_at_position = countOverlaps(position_ranges, grange …
- 4,875
3
votes
Accepted
Identifying outlier loci in R
As Devon said, removing the which will give you W as a logical vector that can be used to index the sorted p-values. To get a logical vector that can be used to subset the original (unsorted) values y …
- 4,875
4
votes
Multiple sequence alignment with R
The ‹msa› package on Bioconductor does exactly that.
It doesn’t hand the results on a silver platter, though: you’ll need to read the vignette carefully to learn how to use it. But after that it’s pr …
- 4,875
6
votes
Accepted
Off-by-one error when mapping Ensembl IDs to gene symbols
There’s no 1:1 mapping between the IDs of different database schemas. As a consequence, some Ensembl gene IDs map to multiple MGI symbols, or to none (and vice versa).
Therefore, you can’t assume tha …
- 4,875
13
votes
What methods are available to find a cutoff value for non-expressed genes in RNA-seq?
I'd like to find genes that were not expressed in a group of samples and were expressed in another group.
This is, fundamentally, a differential expression analysis, with a twist. To solve this, …
- 4,875
18
votes
R package development: How does one automatically install Bioconductor packages upon package...
As suggested, here’s an example showing the relevant lines from a DESCRIPTION file from a CRAN/GitHub hosted project that has Bioconductor dependencies (truncated):
Depends:
R (>= 3.3.0)
biocViews …
- 4,875
9
votes
0
answers
512
views
How can I read multiple different regions from a BAM file in R?
Since the process function is nontrivial and written in R, I’m stuck with R for now. And there’s no reason why this shouldn’t work in R.
Am I overlooking something? Is this a bug in {Rsamtools}? …
- 4,875
2
votes
Accepted
Write the output of the VariantAnnotation package to file
Is there any way to force R to give me the same representation as head?
head just cuts off everything after the first six entries. …
- 4,875
4
votes
How to subset a GRanges via an argument passed into a function?
In addition to Devon’s answer, you can use non-standard evaluation to make this work with R symbol names rather than string arguments:
subsetter = function (gr, cname) {
cname = as.character(substitute …
- 4,875
3
votes
Combine Fastq by writeFastq is not working properly
Apart from this, your R code contains several errors. For instance, your variable names change throughout, and you’re using the fsep parameter wrongly. …
- 4,875
6
votes
How can I extract normalized read count values from DESeq2 results?
It depends what you mean by “normalised”. As Devon said, the normalized = TRUE argument to the count function gives you normalised counts. However, these are “only” library-size normalised (i.e. divid …
- 4,875
6
votes
Accepted
Is there an efficient way to check an input BAM in R?
For a very quick check™ you could also pass the file through gunzip and test whether the “magic bytes” at the beginning of the file equal 'BAM\1':
bgzf_stream = gzfile(filename, 'r')
on.exit(close(bgzf_stream …
- 4,875
32
votes
Accepted
9
votes
What are the ways to keep track of branches in the analysis?
or in a declarative workflow.2
Document the alternative analysis approaches; once again, this could be a declarative workflow with different rules for alternative analyses, or a set of notebooks (via R … This is much harder in R Markdown.
Some time ago I create an example analysis workflow to show how this can be structured. …
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