Closed RuoxinLi closed 5 years ago
Hi @RuoxinLi
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: scBFA
Version: 0.99.91
Date: 2019-03-09
Title: A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq
Description: This package is designed to model gene detection pattern of scRNA-seq through a binary factor analysis model. This model allows user to pass into a cell level covariate matrix X and gene level covariate matrix Q to account for nuisance variance(e.g batch effect), and it will output a low dimensional embedding matrix for downstream analysis.
Authors@R:
c(person(given = "Ruoxin",
family = "Li",
role = c("aut", "cre"),
email = "uskli@ucdavis.edu"),
person(given = "Gerald",
family = "Quon",
role = c("aut"),
email = "gquon@ucdavis.edu"))
URL: https://github.com/ucdavis/quon-titative-biology/BFA
BugReports: https://github.com/ucdavis/quon-titative-biology/BFA/issues
biocViews: SingleCell, Transcriptomics, DimensionReduction,GeneExpression, ATACSeq, BatchEffect, KEGG, QualityControl
Depends: R (>= 3.5)
Imports: SingleCellExperiment,
SummarizedExperiment,
Seurat,
MASS,
zinbwave,
stats,
Suggests:
knitr,
rmarkdown,
testthat,
Rtsne,
ggplot2
VignetteBuilder: knitr
SystemRequirements: R(>=3.5)
RoxygenNote: 6.1.1
License: GPL-3
LazyData: true
Encoding: UTF-8
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Your package has been built on Linux, Mac, and Windows.
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Received a valid push; starting a build. Commits are:
34d50e8 import copula 10060bf import functions built in copula before running ex... e002de5 make example dataset smaller insimulation to speed... 1f36bda remove zinb object b39fc21 document example dataset exprdata.rda ab01500 speed up vignette a14f973 add small example scRNA-seq data 1b20df9 update package version and man pages
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "skipped, ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "skipped, ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS, skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
Received a valid push; starting a build. Commits are:
1574337 correct version number 0.99.914
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "WARNINGS, skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
Hi, It seems my package already passed the windows and linux system check, but for OS system, it outputs the error: dependency copula is not available for package scBFA. Can you help me install it on it? Thanks!
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
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Hi Rita, @RuoxinLi When checking the package, I get an error:
> scData = CreateSeuratObject(raw.data = GeneExpr,project = "sc",min.cells = 0)
Error in CreateSeuratObject(raw.data = GeneExpr, project = "sc", min.cells = 0) :
unused argument (raw.data = GeneExpr)
Execution halted
Please fix this issue, it seems like the argument should be counts
.
Best, Marcel
Hi Marcel,
Thank you for pointing out, I think this is due to seurat's recent update. I will adjust my code accordingly ASAP.
Best Rita
Hi Rita, @RuoxinLi Any updates on the status? Thanks, Marcel
Hi Marcel,
Sorry was focusing on the reviews of BFA main paper recently.
Will address it this weekend
Thanks for the reminder
Best
Rita
On Apr 26, 2019, at 2:19 PM, Marcel Ramos notifications@github.com wrote:
Hi Rita, @RuoxinLi https://github.com/RuoxinLi Any updates on the status? Thanks, Marcel
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/1054#issuecomment-487204843, or mute the thread https://github.com/notifications/unsubscribe-auth/ACZUMCZK6OI2RV2AXKXXY4DPSNWXFANCNFSM4HALKYUA.
Hi Rita, @RuoxinLi Any updates on the status of the package? Thank you. -Marcel
Hi Marcel, I am very sorry. We are busy on addressing the reviewers comments right now, but I will make updates within this week!
Sorry for the delay.
On May 7, 2019, at 12:58 PM, Marcel Ramos notifications@github.com wrote:
Hi Rita, @RuoxinLi https://github.com/RuoxinLi Any updates on the status of the package? Thank you. -Marcel
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/1054#issuecomment-490233082, or mute the thread https://github.com/notifications/unsubscribe-auth/ACZUMC7ESC2G56UZ45IXDG3PUHNPBANCNFSM4HALKYUA.
Hi Rita, @RuoxinLi It has been quite a while. Please provide any updates that you may have. Thank you, Marcel
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
Hi Marcel, @LiNk-NY sorry for the late update, can we start again on the review process, I updated the new version I had so far.
Thank you.
Rita
Hi Marcel, @LiNk-NY, again I apologize for the delay of updating and we were too busy to address the reviewer's comments within given deadlines, so I missed your last comments. Can we start the review process again?
Thank you.
Rita
Hi Rita, @RuoxinLi Did you push a version bump of the package? Thanks, Marcel
Hi Marcel, @LiNk-NY The version I pushed is 0.99.914
Thanks
Hi Rita, @RuoxinLi
Thank you for your submission. Please see the review below. If you have any questions, post them here in the thread.
Best, Marcel
SummarizedExperiment
or
SingleCellExperiment
for the access functions like mcols
, colData
, etc.envir
argument for loading the data
. This might
confuse users. Keep it in the .GlobalEnv
.Minor:
eval=FALSE
;
)[[<-
instead of $
to replace
values programatically (see R/BFA.R
)print
and use message
insteadscbfa
function as the
method
argument and diagnose
function (disperType
), you may also want to
create a vector of methods available and use match.arg
in the body of the
function to match the first one by defaultis
or is.*
derivatives to check class membership instead of
class(x) == "xx"
. You can also create a helper function to extract the
data matrix from these classes (and a check and error message for unsupported
classes)R/data.R
)scNoiseSim
?Minor:
TRUE
twice: if (modelEnv$updateCellcoef == TRUE)
.
Simply use if (modelEnv$updateCellcoef)
<-
as assignment operator (optional)identical
for scalar matching of strings, e.g.,
identical(diagnose_feature, "dispersion")
Thanks Marcel!
On Jul 15, 2019, at 11:05 AM, Marcel Ramos notifications@github.com wrote:
Hi Rita, @RuoxinLi https://github.com/RuoxinLi Thank you for your submission. Please see the review below. If you have any questions, post them here in the thread.
Best, Marcel
scBFA #1054 https://github.com/Bioconductor/Contributions/issues/1054 DESCRIPTION
You may want to depend on either SummarizedExperiment or SingleCellExperiment for the access functions like mcols, colData, etc. NAMESPACE
Looks neat vignettes
You don't need to use an envir argument for loading the data. This might confuse users. Keep it in the .GlobalEnv. Minor:
Use the standard R code chunk for installation instructions and use eval=FALSE R
Avoid using semicolons (;) You can avoid repetitive code by using the [[<- instead of $ to replace values programatically (see R/BFA.R) Avoid using print and use message instead Document all methods available for input to the scbfa function as the method argument and diagnose function (disperType), you may also want to create a vector of methods available and use match.arg in the body of the function to match the first one by default Use is or is.* derivatives to check class membership instead of class(x) == "xx". You can also create a helper function to extract the data matrix from these classes (and a check and error message for unsupported classes) Data documentation looks good (R/data.R) Why not return a standard Bioconductor object from scNoiseSim? Minor:
No need to evaluate TRUE twice: if (modelEnv$updateCellcoef == TRUE). Simply use if (modelEnv$updateCellcoef) Consistently use <- as assignment operator (optional) Use identical for scalar matching of strings, e.g., identical(diagnose_feature, "dispersion") — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/1054?email_source=notifications&email_token=ACZUMC4KM7NMZFPKH7IME4LP7S343A5CNFSM4HALKYUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZ6QACQ#issuecomment-511508490, or mute the thread https://github.com/notifications/unsubscribe-auth/ACZUMC32BV46NSV6IS6JO6LP7S343ANCNFSM4HALKYUA.
Received a valid push; starting a build. Commits are:
a2c588c version 0.99.915 446dc3e return bioconductor object from scNoiseSim 064d73f remove usage of envir argument for loading the dat... 3d19169 address reviewers' comments 2d91b27 return a standard Bioconductor object from scNois... 5a89a0d updating man pages
Hi Marcel, @LiNk-NY, I corrected the scBFA R package based on your comments, however there are two points:
You can avoid repetitive code by using the [[<- instead of $ to replace values programatically (see R/BFA.R) The modification for this comment I made is replace: modelEnv$AA <- param$AA modelEnv$ZZ <- param$ZZ modelEnv$beta <- param$beta modelEnv$gamma <- param$gamma modelEnv$UU <- matrix(param$UU,ncol = 1) modelEnv$VV = matrix(param$VV,ncol = 1) to: for(vNames in c("AA","ZZ","beta","gamma")){ modelEnv[[vNames]] = param[[vNames]] } for(Intercept in c("UU","VV")){ modelEnv[[Intercept]] = matrix(param[[Intercept]],ncol = 1) } But there are other places, like in the initialization, the evaluation for every variable is different, so I keep it unchanged, is it ok?
Document all methods available for input to the scbfa function as the method argument and diagnose function (disperType), you may also want to create a vector of methods available and use match.arg in the body of the function to match the first one by default
Do you mean document the internal function like neg_loglikelihood() , gradient()? Or you mean document the parameter of scbfa like scData, numFactors, etc? Can you give me a simple example?
Thank you!
Best!
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
Hi Rita, @RuoxinLi
- You can avoid repetitive code by using the [[<- instead of $ to replace values programatically (see R/BFA.R) The modification for this comment I made is replace: modelEnv$AA <- param$AA modelEnv$ZZ <- param$ZZ modelEnv$beta <- param$beta modelEnv$gamma <- param$gamma modelEnv$UU <- matrix(param$UU,ncol = 1) modelEnv$VV = matrix(param$VV,ncol = 1) to: for(vNames in c("AA","ZZ","beta","gamma")){ modelEnv[[vNames]] = param[[vNames]] } for(Intercept in c("UU","VV")){ modelEnv[[Intercept]] = matrix(param[[Intercept]],ncol = 1) } But there are other places, like in the initialization, the evaluation for every variable is different, so I keep it unchanged, is it ok?
That's okay, thanks for making the change.
- Document all methods available for input to the scbfa function as the method argument and diagnose function (disperType), you may also want to create a vector of methods available and use match.arg in the body of the function to match the first one by default
Do you mean document the internal function like neg_loglikelihood() , gradient()? Or you mean document the parameter of scbfa like scData, numFactors, etc? Can you give me a simple example?
This means that the diagnose function should look like:
diagnose <- function(scData,
sampleInfo = NULL, disperType = c("Fitted", "Map", "GeneEst"),
diagnose_feature="dispersion")
{
match.arg(disperType, c("Fitted", "Map", "GeneEst"))
...
}
So that your users can see all the possible inputs. I would also add an error message to disperType
not supported. The same would apply to the scbfa
function.
Consider also matching case between the main function and the package name, i.e., scBFA::scBFA
.
Best, Marcel
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on Linux, Mac, and Windows.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
Hi Marcel, @LiNk-NY, I finished the changes based on your previous comments.
Thanks
Best
Rita
Hi Rita, @RuoxinLi Thank you for your contribution. Your package has been accepted.
As you continue to maintain your package please include the minor detail below:
disperType = c("Fitted", "Map", "GeneEst")
. Best regards, Marcel
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