User: Nathaniel Hayden

gravatar for Nathaniel Hayden
Nathaniel Hayden ♦♦ 180
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180
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United States
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2 years, 4 months ago
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2 years, 10 months ago
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Posts by Nathaniel Hayden

<prev • 21 results • page 1 of 3 • next >
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Answer: A: How can I add rows to a dataframe in an HDF5 file using rhdf5?
... The issue here is at the time of this writing rhdf5 treats data.frames specially (writing as COMPOUND type by default) and COMPOUND data types are opaque to rhdf5 (again, at time of this writing). See compoundAsDataFrame and DataFrameAsCompound in ?h5write. Compound types are all-or-nothing; subsett ...
written 2.4 years ago by Nathaniel Hayden ♦♦ 180
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Answer: A: Perform a pileup on the last nucleotides of each read with variable length reads
... Since my original answer (wherein I suggested two workarounds: https://support.bioconductor.org/p/68681/#68716 ) I have added support for reverse bins to pileup. The convention is to use -1 to indicate last nucleotide, -2 second-to-last, etc. I updated the man page and added a couple examples. To ta ...
written 2.4 years ago by Nathaniel Hayden ♦♦ 180
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Answer: A: Perform a pileup on the last nucleotides of each read with variable length reads
... Update 2: I have since updated pileup to allow specifying bins in a strand-sensitive way (query_bins) to respect the actual order of cycles as they came off the sequencer (because reads aligned to the minus strand are "reversed") and allow specifying bins in a strand-insensitive way (left_bins) to p ...
written 2.4 years ago by Nathaniel Hayden ♦♦ 180
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Comment: C: Comparing read sequence back to reference sequence
... Hi, Sam. Your question deserves its own top-level post. I didn't see this until today (and only because someone pointed it out to me) because it was a comment, so I didn't get a notification for it. Could you post a separate question for this and give more information surrounding your use case? And ...
written 2.4 years ago by Nathaniel Hayden ♦♦ 180
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Comment: C: Error installing cn.mops and Rsamtools in R 3.1.3
... OK, from what you said it sounds like you were able to successfully compile with either g++ or R CMD g++? The distinction is important. And it's correct that the program shouldn't produce any output, we're just seeing if g++ (1) finds the standard library headers and (2) links to the C++ standard li ...
written 2.6 years ago by Nathaniel Hayden ♦♦ 180
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Comment: C: Error installing cn.mops and Rsamtools in R 3.1.3
... If which g++ and R CMD which g++ give the same result that tells you the g++ R points to and the g++ you get when you type g++ at the command line are the same. ...
written 2.6 years ago by Nathaniel Hayden ♦♦ 180
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Answer: A: Error installing cn.mops and Rsamtools in R 3.1.3
... Hi, Bill. Are you on a managed system such as a cluster where there might be a non-standard setup? If you are on such a system I recommend talking to your sysadmin, as it doesn't appear to be a problem with the packages you're trying to install. At first blush it looks like your g++ doesn't have th ...
written 2.6 years ago by Nathaniel Hayden ♦♦ 180
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Comment: C: Reading Strings from MAT Files using rhdf5
... I'm wondering if there are encoding issues. raw type, as one might predict, expects everything to be in byte range, i.e., 0 <= x <= 255. Try this in an R session: val <- as.raw(c(0, -21, 42, 255, 256)) # same warning you get as.raw(val) # same error you get And the man page for rawToCha ...
written 2.7 years ago by Nathaniel Hayden ♦♦ 180
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Comment: C: Installation error RBGL 1.42
... Do you know if there has been trouble on this cluster compiling packages containing C++ code that uses #include <iostream>? I think there's a mismatch in your version of gcc and libc or you have a bad install of gcc. More specifically, I think the gcc you get when you compile was built with an ...
written 2.8 years ago by Nathaniel Hayden ♦♦ 180
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Answer: A: rhdf5 package and arrays in R
... Just reference, rhdf5 does not have problems with arrays: > library(rhdf5) > a = array(seq(1.1, 24.1, 1.0), c(2, 3, 4)) > h5fl <- tempfile() > h5createFile(h5fl) [1] TRUE > h5createDataset(h5fl, "a", c(2, 3, 4), storage.mode="double") [1] TRUE > h5write(a, h5fl, "a") > h5du ...
written 2.8 years ago by Nathaniel Hayden ♦♦ 180

Latest awards to Nathaniel Hayden

Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Comparing read sequence back to reference sequence
Scholar 3.0 years ago, created an answer that has been accepted. For A: rhdf5 missing information in read
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: rhdf5 missing information in read
Scholar 3.1 years ago, created an answer that has been accepted. For A: rhdf5 missing information in read

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