User: Michael Steinbaugh

Reputation:
30
Status:
New User
Location:
Harvard
Website:
https://steinbaugh.com/
Twitter:
mjsteinbaugh
Scholar ID:
Google Scholar Page
Last seen:
3 days, 11 hours ago
Joined:
3 years, 2 months ago
Email:
m***@steinbaugh.com

Posts by Michael Steinbaugh

<prev • 22 results • page 1 of 3 • next >
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Comment: C: Correct way to split and unsplit a DataFrame
... Perfect, thanks Michael! ...
written 26 days ago by Michael Steinbaugh30
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Comment: C: Correct way to split and unsplit a DataFrame
... The `stack()` function also gets close but doesn't unsplit back to the original `DataFrame` unmodified: ``` help(topic = "SplitDataFrameList", package = "IRanges") stack(x = split, index.var = ".idx") ``` ``` DataFrame with 4 rows and 3 columns .idx a b C a 3 ...
written 29 days ago by Michael Steinbaugh30
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Correct way to split and unsplit a DataFrame
... I'm having trouble splitting and unsplitting a `DataFrame`, using the methods defined in IRanges. Here's an attempt at a minimal reprex. ```r library(IRanges) df <- DataFrame( a = seq_len(4L), b = as.factor(rep(c("b", "a"), each = 2L)), row.names = LETTERS[seq_len(4L)] ) print(df) `` ...
iranges s4vectors written 29 days ago by Michael Steinbaugh30 • updated 28 days ago by Michael Lawrence11k
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Comment: C: Install Bioconductor 3.7
... It could be an issue specific to rocker/r-ver. Here's a minimal reproducible example. Dockerfile: ``` FROM rocker/r-ver:3.5.3 WORKDIR /tmp ADD install.R . RUN R -f install.R WORKDIR / ``` Corresponding install.R file: ``` install.packages("BiocManager") BiocManager::install(version = "3.7") ``` ...
written 4 months ago by Michael Steinbaugh30
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Comment: C: Install Bioconductor 3.7
... I copied the error from my Docker build, see below ...
written 4 months ago by Michael Steinbaugh30
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Comment: C: Install Bioconductor 3.7
... Thanks, Lori and Martin, I figured it out. For reference, on R 3.5, here's how to install Bioconductor 3.7 or 3.8. Install Bioconductor 3.7: ```r source("https://bioconductor.org/biocLite.R") BiocInstaller::biocLite() ``` Install Bioconductor 3.8: ```r install.packages("BiocManager") BiocManager ...
written 4 months ago by Michael Steinbaugh30
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Comment: C: Install Bioconductor 3.7
... Thanks @shepherl, yeah I might just end up using the versioned release_core2 images as the base instead. I was just wondering on a clean R 3.5 installation, what's the right way to install BioC 3.7 specifically -- I can only get it to install 3.8 at the moment. ...
written 4 months ago by Michael Steinbaugh30
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Install Bioconductor 3.7
... I'm interested in creating versioned Docker images of Bioconductor releases back to 3.6 for unit testing against my package code. I'm stuck getting Bioconductor 3.7 to install instead of 3.8 on R 3.5 using a [rocker/r-ver](https://hub.docker.com/r/rocker/r-ver) base image (e.g. R 3.5.3). What's the ...
docker biocmanager biocversion written 4 months ago by Michael Steinbaugh30 • updated 4 months ago by Martin Morgan ♦♦ 23k
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Comment: C: DataFrame compatible left_join (merge) operation supporting S4 complex columns t
... Thanks Hervé! That's really clever, and exactly what I'm looking for. Best, Mike ...
written 5 months ago by Michael Steinbaugh30
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DataFrame compatible left_join (merge) operation supporting S4 complex columns that never reorders rows
... Is there a left join operation that works on `DataFrame` class objects and NEVER rearranges the rows? The base merge operation (i.e. `S4Vectors::merge`) currently will reorder rows, even when `sort = FALSE`. ``` # This supports S4 columns but will flip rows. m <- S4Vectors::merge( x = x, y = ...
s4 merge dataframe left_join written 5 months ago by Michael Steinbaugh30 • updated 5 months ago by Hervé Pagès ♦♦ 14k

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