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Create slots for both in Expression object, and populate on data load
Change existing summary_frame
to summarize_libraries
method.
Create new summarize_reference
method that provides details on the number of reference genes by protein coding, rRNA, etc.
Create function summary_libraries
based on existing manuscript code that creates a summary data frame of stats for each expression library in a list of Expression
objects.
Create function summary_references
that creates a summary data frame of reference stats from a list of Expression
objects.
Add more tests to evaluate successful parsing of nhx fields and their addition to the nhx@phylo tree.
The species name is recorded as $species_name
in the input son, not $species
. The latter used to work, probably due to partial matching, but doesn't always now. See line 118 here - https://github.com/caseywdunn/agalmar/blob/master/R/utility_functions.R
Sam Church noted the following, and I have seen it as well:
If you load agalmar first then you get a warning:
Found more than one class "DGEList" in cache; using the first, from namespace 'agalmar'
Where if you load edgeR first you still get a warning but it uses the namespace 'edgeR'. The problem is that some of the subsequent analyses I want to perform choke if DGEList comes from agalmar.
Here is the example line of code I want to apply - it corresponds to some of the code originally in the gene expression commands used with agalma, and the purpose is to process the json file and keep only the libraries for the desired treatments.
e <- mclapply(ag.data, Expression, mc.cores=1)
x <- e$whole_embryonic
y <- x@dge
treatments <- x@treatments
focal_treatments = c("Anterior_zero_two","Posterior_zero_two")
keep <- ( treatments %in% focal_treatments )
y <- y[,keep]
If DGEList comes from agalmar, then I get the error 'incorrect dimensions'
At present the DESeq2::DESeqDataSetFromMatrix()
constructor call is in the agalmar Expression()
constructor. Unlike edgeR, the DESeq2 constructor runs the analysis given a particular model.
Move DESeq2::DESeqDataSetFromMatrix()
to a separate method that returns a DESeq2 object given a specified model. Call the new method create_DESeq2(design)
At present gene trees are only parsed in newick format. Parse in nhx format to preserve information on duplications etc.
A few packages do this, including ggtree: https://bioconductor.org/packages/release/bioc/vignettes/ggtree/inst/doc/treeImport.html#parsing-nhx-tree
Hi! Not really an issue because I was able to fix, so feel free to close. Wanted to share here in case it helps anyone. Looking forward to exploring functions in this package. Thank you!
Installing in RStudio (MacOS 10_13_3, RStudio 1.1.383, R 3.4.2) with:
install_github('caseywdunn/agalmar')
Fixed with this from recommendation:
install.packages("base64enc", type = "binary")
install.packages("jsonlite", type="binary")
install.packages("rmarkdown")
devtools::install_github("tidyverse/reprex")
source("https://bioconductor.org/biocLite.R")
biocLite("treeio")
install_github('caseywdunn/agalmar')
Error messages:
> install_github('caseywdunn/agalmar')
Downloading GitHub repo caseywdunn/agalmar@master
from URL https://api.github.com/repos/caseywdunn/agalmar/zipball/master
Installing agalmar
Downloading GitHub repo caseywdunn/hutan@master
from URL https://api.github.com/repos/caseywdunn/hutan/zipball/master
Installing hutan
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore \
--quiet CMD INSTALL \
'/private/var/folders/5m/37fhf86x0g70t9w632_f9yf80000gn/T/RtmpCHxgE5/devtools875e654ab908/caseywdunn-hutan-ff536f3' \
--library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' --install-tests
* installing *source* package ‘hutan’ ...
Warning in as.POSIXlt.POSIXct(x, tz) :
unknown timezone 'zone/tz/2018c.1.0/zoneinfo/America/Los_Angeles'
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (hutan)
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore \
--quiet CMD INSTALL \
'/private/var/folders/5m/37fhf86x0g70t9w632_f9yf80000gn/T/RtmpCHxgE5/devtools875e4bfb0cb8/caseywdunn-agalmar-33d5a33' \
--library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' --install-tests
ERROR: dependency ‘treeio’ is not available for package ‘agalmar’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/agalmar’
Installation failed: Command failed (1)
Tried biocLite("treeio")
with the following error:
ERROR: dependency ‘rmarkdown’ is not available for package ‘reprex’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/reprex’
The downloaded source packages are in
‘/private/var/folders/5m/37fhf86x0g70t9w632_f9yf80000gn/T/RtmpCHxgE5/downloaded_packages’
Warning message:
In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘reprex’ had non-zero exit status
Tried install.packages("reprex")
with the following error:
ERROR: dependency ‘rmarkdown’ is not available for package ‘reprex’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/reprex’
Warning in install.packages :
installation of package ‘reprex’ had non-zero exit status
Replace plyr::ldply
calls
The newest version of Agalma includes fpkm and gene length outputs that need to be parsed - add lengths, fpkm to setClass
and to the function
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