The package is not yet available from Bioconductor.
Install the development version of the AnVILAz package from GitHub with
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager", repos = "https://cran.r-project.org")
BiocManager::install("Bioconductor/AnVILAz")
Once installed, load the package with
For this tutorial we will refer to the Azure Blob Storage service as ABS. Within the ABS, we are given access to a Container. For more information, follow this link to Microsoft’s definition of containers and blobs.
The avlist
command corresponds to a view of the files in
the Blob container on Azure. They can also be accessed via the Microsoft
Azure Storage Explorer.
As an example, we load the internal mtcars
dataset and
save it as an .Rda
file with save
. We can then
upload this file to the ABS.
Now we can upload the data to the analyses/
folder in
the Azure Blob Storage (ABS) Container.
We can also use a small log file for demonstration purposes. The
jupyter.log
file is already present in our workspace
directory.
We can remove the data with avremove
and the
relative path to the .Rda
file.
The reverse operation is also possible with a remote and local paths as the first and second arguments, respectively.
To upload an entire folder, we can use avbackup
. Note
that the entire test
folder becomes a subfolder of the
remote analyses
folder in this example.
By default, the entire source
directory will be copied
to the current working directory "."
, i.e., the base
workspace directory.
You may also move this to another folder by providing a folder name as the second argument.
DATA
tabmtcars
exampleFirst we create an example dataset for uploading to the
DATA
tab. We create a model_id
column from the
rownames
.
The avtable_import
command takes an existing R object
(usually a tibble
) and uploads to the DATA
tab
in the AnVIL User Interface. The table
argument will set
the name of the table. We also need to provide the
primaryKey
which corresponds to the column name that
uniquely identifies each row in the data. Typically, the
primaryKey
column provides a list of patient or UUID
identifiers and is in the first column of the data.
The avtable
function will pull the data from the
DATA
tab and represent the data locally as a
tibble
. It works by using the same type
identifier (i.e., the table
argument) that was used when
the data was uploaded.
The API allows deletion of specific rows in the data using
avtable_delete_values
. To indicate which row to delete,
provide the a value or set of values that correspond to row identifiers
in the primaryKey
. In this example, we remove the
AMC-Javelin
entry from the data. We are left with 31
records.
If you experience issues, please feel free to contact us with a reproducible example on GitHub:
## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] AnVILAz_1.1.0 BiocStyle_2.33.1
##
## loaded via a namespace (and not attached):
## [1] vctrs_0.6.5 httr_1.4.7 cli_3.6.3
## [4] knitr_1.48 rlang_1.1.4 xfun_0.48
## [7] jsonlite_1.8.9 glue_1.8.0 rjsoncons_1.3.1
## [10] buildtools_1.0.0 htmltools_0.5.8.1 maketools_1.3.1
## [13] BiocBaseUtils_1.7.3 sys_3.4.3 sass_0.4.9
## [16] fansi_1.0.6 rappdirs_0.3.3 rmarkdown_2.28
## [19] tibble_3.2.1 evaluate_1.0.1 jquerylib_0.1.4
## [22] fastmap_1.2.0 yaml_2.3.10 lifecycle_1.0.4
## [25] httr2_1.0.5 BiocManager_1.30.25 compiler_4.4.1
## [28] pkgconfig_2.0.3 digest_0.6.37 R6_2.5.1
## [31] utf8_1.2.4 pillar_1.9.0 magrittr_2.0.3
## [34] bslib_0.8.0 tools_4.4.1 AnVILBase_0.99.32
## [37] cachem_1.1.0