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multimir's Introduction

multiMiR

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2023 DB update is coming July 2024 (Thank you for your patience) - Please comment to provide feedback

The multiMiR web server hosts a database containing miRNA-target interactions from external databases. The package multiMiR provides functions to communicate with the multiMiR web server and its database.

Note this repository is where active development occurs (think 'nightly' builds). The recommended release and devel versions are available via Bioconductor (as of Bioconductor 3.6).

# To install multiMiR, use BiocManager::install()
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install()
BiocManager::install("multiMiR")

Terminology used in package:

  • sql components: SELECT or FROM or ON or WHERE... etc. (mmsql_components class)
  • sql features: specific to this DB and the options used to generate meaningful queries (i.e. mirna; conserved; table type: validated, predicted; etc.)
  • sql: a complete sql statement (mmsql class)
  • query: table result of sql statement (mmquery class), class includes sql statement and parts.

* Warning * There are issues with merging target IDs from older unmaintained databases. Databases that have been updated more recently (1-2 years) use current versions of annotated IDs. In each update these old target IDs are carried over due to a lack of a reliable method to disambiguate the original ID with current IDs. Please keep this in mind with results from older databases that have not been updated. We continue to look at methods to resolve these ambiguities and improve target agreement between databases. You can use the unique() R function to identify and then remove multiple target genes if needed.

multimir's People

Contributors

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Watchers

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Forkers

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multimir's Issues

Time out using get_multimir with 'predicted' parameter

Running get_multimir with table='predicted' as such:
predicted = get_multimir(mirna = expt_miRNAs, org = 'mmu', summary = TRUE, table = 'predicted')
Gets stuck at 'Searching targetscan ...'

However running:
targetscan = get_multimir(mirna = expt_miRNAs, org = 'mmu', summary = TRUE, table = 'targetscan')
Runs to completion.

Investigate options for passing URLs used throughout package functions

Currently uses a variable local to the package environment. Using getOption to access and options("" = ...) to set may be advantageous in that it:

  1. formalizes the URLs as key package options
  2. allows the user to update the URL (universally across the R session) without requiring a new package release
  3. prevents confusion over local vs package environment variable
# 2. 
options("multimir_URL" = "https://new-mm-url.edu")
multimir_dbInfo()  # Still works without passing the new URL each time

# 3.
multimir_URL  # Variable found in package environment
# [1] "http://multimir.ucdenver.edu/cgi-bin/multimir.pl"
multimir_URL <- "test"  # User attempt to update value places it in local environment
multimir_URL      # User/global environment
# [1] "test"
multiMiR::multimir_URL # But actual value used in functions (package env) is unchanged
# [1] "http://multimir.ucdenver.edu/cgi-bin/multimir.pl"
>

Score integration

Dear authors,

I'm still working with your package to analyse massively miRNA-targets interactions and I would like to suggest for you to incorporate an integrated prediction score to your package. Using this every user can compare the same miRNA-target interaction between different prediction databases. Currently each database has a different range of scores in the same dataframe column and this can be a problem when comparing between databasets.

Kindest regards

Katerina's revisions

  1. Send to Kevin as well, to keep him in the looop

  2. Can you reference our paper (provide link to PubMed) in the Vignette? Unless there is a rule about that. Maybe in the introduction when you introduce the webserver?

  3. You know more about making vignettes, but what is the rationale for some output that is displayed but not others? For example, should the output for other "db.ver", "db.tables", "apply(db.count[,-1], 2, sum)" etc. commands in the "Getting to know ..." section be displayed? You show output for other sections (like the examples).

  4. For the "Luciferase" and "cisplatin" searches, can the function handle case insensitive?

Minor comments:

  1. Some language edits in the "Getting to know ..." section, please us this instead

Among the 14 external databases, eight contain predicted miRNA-target interactions (DIANA-microT-CDS, ElMMo, MicroCosm, miRanda, miRDB, PicTar, PITA, and TargetScan), three have experimentally validated miRNA-target interactions (miRecords, miRTarBase, and TarBase) and the remaining three contain miRNA-drug/disease associations (miR2Disease, Pharmaco-miR, and PhenomiR). To check these categories and databases from within R, we have a set of four helper functions:

  1. Take out extra "}" for the "List miRNAs ..." header

Handle massive queries

I am trying to perform massive analysis of miRNA targets and I have found your tool very usefull. However, since I am working in a computation cluster, my cluster have limited time to execute at login (This is the only node wit access to internet) and your tool download the queries and format all data to multiMiR format for each database in the same job, I have a lot of troubles to make big queries or complete all the databases. I have tryed to split big queries to many small chunks, but the attempt was not successful. Can you recommend me any solution for my problem? I suggest you to divide get_multimir function in diferent modes:
i) query all databases and save the raw data to a temporal folder
ii) give to get_multimir the temporal folder and the function format this data to multiMiR layout instead of download the data.
In this way, I can download the without the CPU workload and then process all the data in my cluster without interruption issues. Also, it would be a great feature, an user can make a generic query and download it. Then, make more specific queries onto the downloaded data tuning the parameters without stressing the databases APIs queried by your package so the user would identify faster its ideal setting.

Fix error in citation() function 

citation("multiMiR")
# To cite package ‘multiMiR’ in publications use:
# 
#   Yuanbin Ru and Katerina Kechris (2016). multiMiR: Integration of
#   multiple microRNA-target databases with their disease and drug
#   associations. R package version 0.98.0.1.
# 
# A BibTeX entry for LaTeX users is
# 
#   @Manual{,
#     title = {multiMiR: Integration of multiple microRNA-target databases with their
# disease and drug associations},
#     author = {Yuanbin Ru and Katerina Kechris},
#     year = {2016},
#     note = {R package version 0.98.0.1},
#   }
# 
# ATTENTION: This citation information has been auto-generated from the
# package DESCRIPTION file and may need manual editing, see
# ‘help("citation")’.
# 
# Warning message:
# In citation("multiMiR") :
#   no date field in DESCRIPTION file of package ‘multiMiR’

Resolve truncated example code

Via TravisCI build log:

Rd file 'search.multimir.Rd':
\examples lines wider than 100 characters:
result <- search.multimir(query="select m.mature_mirna_acc, m.mature_mirna_id, t.target_symbol, t.target_entrez, t.target_ensembl, i. ... [TRUNCATED]
These lines will be truncated in the PDF manual.

I'd prefer limiting linewidth to 80 or 100 character in all documents and code.

Prediction scores from multiMiR output

Sorry to post this again -- I left the same text in a comment, but I wasn't sure if I should post as a new issue. First, I would like to thank your group for making this tool publicly available. My issue is that I am not sure how to interpret the multiMiR output prediction scores: I recognize that each database calculates its own prediction score, but many of them calculate multiple scores and it is unclear which of these the multiMiR output includes. Further, I can't find information about the prediction score calculation for some of the databases (e.g. microcosm). It is difficult to filter by score without knowing what prediction scores signify or the suggested cutoff for the different databases. The information that is available in the Ru et al 2014 multiMiR publication also doesn't seem to align with the multiMiR output I produced in 2019 (i.e., for PITA, the publication discusses a prediction score of 0 to 1, but my prediction scores range from -7 to -22. I assume this is actually PITA's delta delta G score, but I'm not sure. Is this information available somewhere?

connection refused in R

Hi multiMiR team,

I am using the multiMiR package for miRNA target retrieval but there is some problem with the connection to the server.
below is the error message I received:

library(multiMiR)
Error: package or namespace load failed for ‘multiMiR’:
 .onLoad failed in loadNamespace() for 'multiMiR', details:
  call: function (type, msg, asError = TRUE) 
  error: Failed to connect to multimir.org port 80: Connection refused

I posted the question on stackoverflow,
please find a link to my question I asked on Stackoverflow:
question on stackoverflow

There I got a response saying the multimir.org is down temporarily.

I would like your help in this regard.
Looking forward to hearing from you.

Thank you in advance.

Bioconductor reviewer comments

Initial comment:

R1: Obviously needs better integration with Bioconductor.

Me: A little more explanation or an example of how would be greatly appreciated.

R1: We typically expect packages to plug into upstream and downstream workflows. The
vignette shows many ways of retrieving miRNA annotations, etc, but does not give an example of
using them in an actual analysis.

  1. Add an example using other bioconductor packages

R2: Hi,

I've done a first review. A few suggestions and comments below.

(1) BiocCheck output:

Checking for bioc-devel mailing list subscription...
ERROR: Maintainer must subscribe to the bioc-devel mailing list.
Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel

  1. DONE Subscribe to mailing list

(2) Packages in 'Imports' should be fully or partially imported in NAMESPACE.

  1. DONE Look into 'imports' and NAMESPACE

(3) Internal functions

If you don't expect the user to call a function I would not export it. If the function is exported you need a full man page with examples. For example, add.multimir.links.Rd does not have an example.

  1. DONE Reduce number of exported functions

(4) Function names:

Some have underscores, some have dots ("."). It looks like you're using dot for internal functions. If a user can call a function it technically isn't internal. I'd recommend being consistent and using underscores for all exported functions.

  1. DONE Replace dots with underscores in exported functions

(5) Since this package is serving up annotations, they should support the same methods as the other annotations in Bioconductor. Please implement the select() family interface from AnnotationDbi on the objects you return from get.multimir(). The family includes select(), keys(), keytypes() and cols().

  1. Look into adding AnnotationDbi::select(), keys(), keytypes(), and cols() for get.mulitmir() objects

(6) Consider using the AnnotationFilter package for filtering of the results. If you feel you can't implement the filter interface in this package please explain why. The package is fairly new and if there are suggestions to expand compatibility then we'd like to hear them.

  1. Look at AnnotationFilter for filtering results

Let me know if you have questions.

failure when library(multiMiR)

> library(multiMiR) Error: package or namespace load failed for ‘multiMiR’: .onLoad failed in loadNamespace() for 'multiMiR', details: call: function (type, msg, asError = TRUE) error: Recv failure: Connection was reset
R:4.3.0
Rtools:4.3

miRTarBase update request

Dear authors,

We are using your tool for validating miRNA-RNA pairs correlated in expression data.
I have seen that miRTarBase has published two new versions improving the amount of validated pairs: from 595 913 pairs on the 7.0 version to 2 200 449 pairs on 9.0 version.
They have change the URL to https://mirtarbase.cuhk.edu.cn too, here you have the citation https://doi.org/10.1093/nar/gkab1079.
We are wondering if you are including the updates on your tool, are you?

Kindest regards

database update status

Here's the current status of all databases, from the listing at http://multimir.ucdenver.edu. Most of them need updating, obviously. Once I'm added to the project as a contributor, I'll self-assign this issue, and get access from @kechrisk or @smahaffey to update the databases on the server.

Databases that appear to be up to date:

  • miRanda has a current date of August, 2010, which is the same as the latest on the linked database.
  • PITA is currently version 6, same as the latest on the link.
  • PhenomiR has a current date of February 15th, 2011. This appears to be up to date.

Databases that need updating:

Databases with uncertain status:

Databases with broken links:

The first two categories are easy enough to deal with. The third ("uncertain status") may take some more work. And I'm honestly not sure what to say about the fourth ("broken links"). Do we want to leave them as they are? If so, should we warn the user, and maybe provide an option not to use anything that isn't known to be up to date? Something to discuss.

Error with “mmquery_bioc”

example1 <- get_multimir(mirna = 'hsa-miR-18a-3p', summary = TRUE)
Searching mirecords ...
Searching mirtarbase ...
Searching tarbase ...
Error in validObject(.Object) :
invalid class “mmquery_bioc” object: invalid object for slot "summary" in class "mmquery_bioc": got class "NULL", should be or extend class "data.frame"

Add @return to man pages of exported functions

Bioconductor build output (from bioconductor submission, initial build -- speaking of, why does this differs from Travis CI?):

* WARNING: Add non-empty \value sections to the following man
  pages:
  • X man/add.multimir.links.Rd,
  • X man/all_tables.Rd,
  • man/as_mmquery.Rd,
  • man/as_mmsql_components.Rd,
  • man/build_mmsql.Rd,
  • man/default_cutoff.Rd,
  • man/deprecate_arg.Rd,
  • man/get.multimir.cutoffs.Rd,
  • man/multimir.summary.Rd,
  • man/myurlencode.Rd,
  • man/pad.Rd,
  • man/parens_quote.Rd,
  • man/parens_wrap.Rd,
  • man/parse_orgs.Rd,
  • man/parse_response.Rd,
  • man/query_multimir.Rd,
  • man/quote_wrap.Rd,
  • man/remove_empty_strings.Rd,
  • man/remove_table.Rd,
  • man/sql_org.Rd,
  • man/sql_validated.Rd,
  • man/submit_request.Rd

Rmd version of vignette

Advantages: far easier to write and maintain. And IMHO, easier to view and use since an html file and web browser are lighter weight and almost always open on a users computer (as opposed to a PDF file and PDF viewer).

Doing this under BERD time.

TargetScan Prediction Score cutoff interpretation

Hi,

I am trying to derive predicted targets for specific miRNAs. When looking at the targetScan results derived from the multiMir tools in comparision to the one derived from the targetScan website directly, I can not reproduce the results. Could you clarify how the cutoff for the prediction score is derived and how the ranking is done?

Here is the code and results. multiMir v1.20.0

mir <- "mmu-miR-322-3p
predCutoff <- 70
get_multimir(mirna = mir, table   = "predicted", org = "mmu", predicted.cutoff = predCutoff)

database mature_mirna_acc mature_mirna_id target_symbol target_entrez target_ensembl score type
1 targetscan MIMAT0000549 mmu-miR-322-3p Abi3bp 320712 ENSMUSG00000035258 -0.137 predicted
2 targetscan MIMAT0000549 mmu-miR-322-3p Rhoa 11848 ENSMUSG00000007815 -0.155 predicted
3 targetscan MIMAT0000549 mmu-miR-322-3p Ipo7 233726 ENSMUSG00000066232 -0.167 predicted
4 targetscan MIMAT0000549 mmu-miR-322-3p Pik3ca 18706 ENSMUSG00000027665 -0.168 predicted
5 targetscan MIMAT0000549 mmu-miR-322-3p Marcks 17118 ENSMUSG00000069662 -0.168 predicted
6 targetscan MIMAT0000549 mmu-miR-322-3p Elavl4 15572 ENSMUSG00000028546 -0.173 predicted
7 targetscan MIMAT0000549 mmu-miR-322-3p Ywhag 22628 ENSMUSG00000051391 -0.184 predicted
8 targetscan MIMAT0000549 mmu-miR-322-3p Fbxw7 50754 ENSMUSG00000028086 -0.21 predicted
9 targetscan MIMAT0000549 mmu-miR-322-3p Cpeb2 231207 ENSMUSG00000039782 -0.223 predicted
10 targetscan MIMAT0000549 mmu-miR-322-3p Sp3 20687 ENSMUSG00000027109 -0.224 predicted
11 targetscan MIMAT0000549 mmu-miR-322-3p Meis2 17536 ENSMUSG00000027210 -0.228 predicted
12 targetscan MIMAT0000549 mmu-miR-322-3p Tfap2b 21419 ENSMUSG00000025927 -0.237 predicted
13 targetscan MIMAT0000549 mmu-miR-322-3p Hnrnpdl 50926 ENSMUSG00000029328 -0.26 predicted
14 targetscan MIMAT0000549 mmu-miR-322-3p Gpc4 14735 ENSMUSG00000031119 -0.27 predicted
15 targetscan MIMAT0000549 mmu-miR-322-3p Kmt2e 69188 ENSMUSG00000029004 -0.274 predicted
16 targetscan MIMAT0000549 mmu-miR-322-3p Fgf13 14168 ENSMUSG00000031137 -0.277 predicted
17 targetscan MIMAT0000549 mmu-miR-322-3p Zfand4 67492 ENSMUSG00000042213 -0.288 predicted
18 targetscan MIMAT0000549 mmu-miR-322-3p Map2k4 26398 ENSMUSG00000033352 -0.291 predicted
19 targetscan MIMAT0000549 mmu-miR-322-3p Smap1 98366 ENSMUSG00000026155 -0.309 predicted
20 targetscan MIMAT0000549 mmu-miR-322-3p Ube2v2 70620 ENSMUSG00000022674 -0.31 predicted
21 targetscan MIMAT0000549 mmu-miR-322-3p Paip2 67869 ENSMUSG00000037058 -0.405 predicted
22 targetscan MIMAT0000549 mmu-miR-322-3p Nfyb 18045 ENSMUSG00000020248 -0.411 predicted

The scores are comparable for most of the targets but the ranks clearly differ (Cumulative weighted context++ score).

TargetScan7 - https://www.targetscan.org/cgi-bin/targetscan/mmu_71/targetscan.cgi?mirg=mmu-miR-322-3p
filtered results only showing the targets predicted by multiMir

<style> </style>
rank Target gene Representative transcript Representative miRNA Cumulative weighted context++ score Total context++ score
179 Nfyb ENSMUST00000130911.2 mmu-miR-322-3p -0.38 -0.41
214 Ube2v2 ENSMUST00000115777.4 mmu-miR-322-3p -0.35 -0.52
237 Map2k4 ENSMUST00000046963.4 mmu-miR-322-3p -0.34 -0.35
331 Smap1 ENSMUST00000027339.8 mmu-miR-322-3p -0.28 -0.31
334 Fgf13 ENSMUST00000033473.6 mmu-miR-322-3p -0.28 -0.3
373 Cpeb2 ENSMUST00000169035.2 mmu-miR-322-3p -0.27 -0.27
382 Kmt2e ENSMUST00000094962.3 mmu-miR-322-3p -0.26 -0.3
385 Hnrnpdl ENSMUST00000128187.2 mmu-miR-322-3p -0.26 -0.28
388 Sp3 ENSMUST00000102689.4 mmu-miR-322-3p -0.26 -0.27
447 Zfand4 ENSMUST00000036503.8 mmu-miR-322-3p -0.24 -0.3
448 Meis2 ENSMUST00000110907.2 mmu-miR-322-3p -0.24 -0.29
703 Pik3ca ENSMUST00000029201.8 mmu-miR-322-3p -0.19 -0.2
757 Elavl4 ENSMUST00000106598.2 mmu-miR-322-3p -0.18 -0.24
830 Ipo7 ENSMUST00000084731.3 mmu-miR-322-3p -0.17 -0.19
876 Marcks ENSMUST00000092584.5 mmu-miR-322-3p -0.17 -0.17
917 Ywhag ENSMUST00000055808.5 mmu-miR-322-3p -0.16 -0.18
1061 Gpc4 ENSMUST00000033450.2 mmu-miR-322-3p -0.14 -0.32
1086 Rhoa ENSMUST00000007959.8 mmu-miR-322-3p -0.14 -0.15
1750 Paip2 ENSMUST00000041314.9 mmu-miR-322-3p -0.08 -1.07
2454 Tfap2b ENSMUST00000027059.5 mmu-miR-322-3p -0.04 -0.24
3879 Fbxw7 ENSMUST00000107679.2 mmu-miR-322-3p 0 -0.21
3953 Abi3bp ENSMUST00000048471.8 mmu-miR-322-3p 0 -0.14

Error: 'split_by' is not an exported object from 'namespace:purrr'

example1 <- get.multimir(mirna = 'hsa-miR-612', summary = TRUE)
Searching mirecords ...
Searching mirtarbase ...
Searching tarbase ...
Error: 'split_by' is not an exported object from 'namespace:purrr'

And I have try
install.packages("purrr")
library(purrr)

After that it doesn't work as well.

Queries with no records found results in error

Hi guys,

We noticed that a new multiMiR version spits out error when the list is empty.
In previous versions, we have

get.multimir(mirna= "hsa-miR-548h-3p", target = "NTM")
Searching mirecords ...
Searching mirtarbase ...
Searching tarbase ...
list()

In the new version, get.multimir is replaced by get_multimir. We get

get.multimir(mirna= "hsa-miR-548h-3p", target = "NTM")
Searching mirecords ...
Searching mirtarbase ...
Searching tarbase ...
Error: .x is empty, and no .init supplied Called from: reduce_init(.x, .init, left = .left)

Gateway timeout

Hello,

I am consistently getting this error:

get_multimir(mirna=miRNAs$Symbol,table='predicted', org='human')
Searching diana_microt ...
Error: Gateway Timeout

sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS/LAPACK: /opt/miniconda3/envs/R4.0/lib/libopenblasp-r0.3.10.so

locale:
[1] C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] multiMiR_1.12.0

Scores From Prediction Databases?

Hello,

Thanks for creating such a comprehensive database of miRNA-mRNA interactions. I was wondering if you could add some documentation regarding the scores for the prediction databases? I read your original manuscript, and I found the line, "All predicted databases have a primary score for target site strength, which is calculated depending on the particular computational method." Does this mean each score is imported from the respective prediction databases? So that a score from a hit in PicTar would not be comparable to a score from miRanda for the same miRNA-mRNA pair? Or does multiMiR calculate its own confidence score?

Thanks,

Jenny

deprecated 'as_data_frame()'

Hello,
I used multiMiR package 4 months ago, and there was no problem generating the outputs.

But, when I used the same code today, I get the following warning message and I couldn't get the output 'data'.

Warning message:
as_data_frame() was deprecated in tibble 2.0.0.
ℹ Please use as_tibble() (with slightly different
semantics) to convert to a tibble, or as.data.frame()
to convert to a data frame.
ℹ The deprecated feature was likely used in the multiMiR
package.
Please report the issue at
https://github.com/KechrisLab/multiMiR/issues.

Could you check this problem?

Thanks,
Eunbi.

SQL where statements sometimes contain ? instead of values or being left out

in get.multimir.by.Table the query seems to still include organism and possibly other parameters in the where clause if no organism is specified. However this isn't valid and is causing long execution times instead of immediately returning an error. There are if statements so if the parameter is null it should be left out of the query. I suspect somewhere it is being set to a ? or somehow defaulting to that. Need to find a way to make sure parameters are excluded when they are invalid.

What the functional column does mean please

Hello

I have put a lot of miRNAs in your software and I obtained a list of validated target genes for them by

example1 <- get_multimir(mirna = c("hsa-mir-1469",
+ "hsa-mir-12128p"), summary = TRUE)

In supported_type column of the results I see like this

Screenshot 2021-10-04 at 10 30 58

I could not find what each one does mean, like MIT, NEGATIVE, POSITIVE, WEAK, ETC

Could you please help me to get some intuition and ultimately I could refine my results.

Thank you so much in advance

db.info

This database is truly amazing!
I'm already working with it for a while. I just noticed that despite using the db_version = "2.2.0" I have a db.info table for the previous version of the database. For example, db.info shows that last release of TargetScan was 7.1 Jun, 2012. According to your webpage, it should be a version from Jun, 2016.
I tried to reinstall the package couple of times and everything seems ok but this wrong table still appears. How I can be 100% sure that I'm working with the last release of the multiMiR? 2012 is way too much outdated.
I'd be grateful for the help.

Zofia

db_info_error.txt

Failure when receiving data from the peer

Hello,
I used to produce results smoothy by multimir. However, I got the error msg. last night (copied below). I have no idea to figure out. I test the same code on mac and linux. Both of them reported the same error.

Error in map():
ℹ In index: 1.
Caused by error in load():
! cannot open the connection to 'http://multimir.org/multimir_cutoffs_2.3.rda'
Run rlang::last_trace() to see where the error occurred.
Warning message:
In load(url.file) :
URL 'http://multimir.org/multimir_cutoffs_2.3.rda': status was 'Failure when receiving data from the peer'

Issue with get_multimir: table = "predicted"

I have been using this package for the last year and have had no issues executing the "predicted" command allowing to search multiple putative miRNA target databases at once. However, recently I can now only get this function working by selecting one database at a time. Has there been an update? or is this "predicted" now no longer available?

Error with loading multiMiR

I am getting this error when trying to run multiMiR.

Error in load(url.file) :
cannot open the connection to 'http://multimir.org/multimir_cutoffs_2.3.rda'
In addition: Warning message:
In load(url.file) :
URL 'http://multimir.org/multimir_cutoffs_2.3.rda': status was 'Couldn't connect to server'

When I restarted RStudio and ran library(multiMiR), the following is the error that popped up.

Error: package or namespace load failed for ‘multiMiR’:
.onLoad failed in loadNamespace() for 'multiMiR', details:
call: function (type, msg, asError = TRUE)
error: Failed to connect to multimir.org port 80: Connection refused

It would be so kind of you to help me out.

Look at RCurl timeout

I think the timeout for RCurl defaults to 200 seconds which may not be long enough for some requests. I don't think we need to make it as extreme as the server timeout of 30min. We can call it with a specific timeout so maybe changing the default to 10-15 minutes would help support longer queries or we could use some function based on the length of the list to set the timeout. The time required for most requests is related to the length of the list of targets and miRNAs. It can handle a longer list of targets than it can handle a longer list of miRNAs.

However I did try to create appropriate indices for most queries in each table so it should speed queries up.

are there local databases like 'org.Hs.eg.db' for search

Dear author,
It's fancinating to integrated all kinds of miRNAs' resources.
The internet based will highlight the query speed, especially for researchers in China.
So, are there local databases like 'org.Hs.eg.db' for search ?
I had suffered with error 'transfer closed with outstanding read data remaining'.
Thanks.

Website corrections/updates

Via Kevin --

There are a few minor things about the website (multimir.ucdenver.edu), and I wonder if you could help
with them when you have time.

  1. Please update the User's Guide / vignette on the website and in the package - at least add your
    name (and Spencer?) to the author list.
  2. In the "Contributors" section on the website, please add yourself (and Spencer?) in.
  3. In the "Contributors" section, would you mind changing my affiliation to BioMarin Pharmaceutical
    Inc. (www.biomarin.com)?
  4. For the bug report email account ([email protected]), I haven't checked it for a while.
    Would you like to use a different one? If you want to keep it, I will need to recover the password.

Final pre-submission changes

  • Fix documentation for mmquery_bioc-class methods (own generic?).
  • Finish incorporating Brian's code.
  • Add example of AnnoDbi methods to vignette.
  • Add explanation of legacy S3 vs S4.

Update Databases / Add New Databases

We will start work on updating:
miRTarBase – v7 -> v9
TargetScan – v7.2 -> v8

Are there any databases you would like to request? Please comment.

Consider using Roxygen2 for documentation

via Roxygen2 vignette:

Roxygen2 provides a number of advantages over writing .Rd files by hand:

  • Code and documentation are adjacent so when you modify your code, it’s easy to remember that you need to update the documentation.
  • Roxygen2 dynamically inspects the objects that it’s documenting, so it can automatically add data that you’d otherwise have to write by hand.
  • It abstracts over the differences in documenting S3 and S4 methods, generics and classes so you need to learn fewer details.

Can't load library(multiMiR) 

> library(multiMiR)
Error: package or namespace load failed for ‘multiMiR’:
 .onLoad failed in loadNamespace() for 'multiMiR', details:
  call: function (type, msg, asError = TRUE) 
  error: Empty reply from server

Is there something wrong with the server or just my internet? Thank you.

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