Revision of qcscore_model_spe branch - #65

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Revision of qcscore_model_spe branch#65
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CopilotAI commented Jul 24, 2026•
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  • Fixed some issues with QS computation with custom formula;
  • updated QC functions documentation;
  • added more customizable settings to plot functions;
  • function name standardization to Quality Score (QScore);
  • added backward-compatible deprecated wrappers for computeQCScore() and computeQCScoreFlags() following Bioconductor .Deprecated() guidelines;
  • updated vignettes.

CopilotAI mentioned this pull request Jul 24, 2026
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CopilotAI changed the title [WIP] Revision of qcscore_model_spe branchRevision of qcscore_model_spe branchJul 24, 2026
CopilotAI requested a review from drighelliJuly 24, 2026 10:13
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@copilot fix warning and note coming from workflows!
Check consistencies of the function arguments in the function code itself!

❯ checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'plotZoomFovsMap.Rd'
‘csize’ ‘calpha’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
❯ checking R code for possible problems ... NOTE
computeQScore: no visible global function definition for ‘terms’
Undefined global functions or variables:
terms
Consider adding
importFrom("stats", "terms")
to your NAMESPACE file.

CopilotAI commented Jul 24, 2026

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@copilot fix warning and note coming from workflows!
Check consistencies of the function arguments in the function code itself!

...

Fixed both issues in commit Fix R CMD check WARNING and NOTE:

  1. WARNING (plotZoomFovsMap.Rd undocumented args): Removed the unused csize and calpha parameters from the plotZoomFovsMap function signature — they were never used in the function body (equivalent arguments can be passed via ... to plotPolygons if needed).

  2. NOTE (computeQScore: no visible global function definition for 'terms'): Added terms to the @importFrom stats line in QC.R and added importFrom(stats,terms) to NAMESPACE.

@BenedettaBanzi
BenedettaBanzi marked this pull request as ready for review July 24, 2026 15:12
@drighellidrighelli mentioned this pull request Jul 29, 2026
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Revision of qcscore_model_spe branch - #65
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copilot/qcscore-model-spe
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Revision of qcscore_model_spe branch#65
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CopilotAI
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  • Fixed some issues with QS computation with custom formula;
  • updated QC functions documentation;
  • added more customizable settings to plot functions;
  • function name standardization to Quality Score (QScore);
  • added backward-compatible deprecated wrappers for computeQCScore() and computeQCScoreFlags() following Bioconductor .Deprecated() guidelines;
  • updated vignettes.
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[WIP] Revision of qcscore_model_spe branchRevision of qcscore_model_spe branchJul 24, 2026
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@copilot fix warning and note coming from workflows!

Check consistencies of the function arguments in the function code itself!
❯ checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'plotZoomFovsMap.Rd'
‘csize’ ‘calpha’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
❯ checking R code for possible problems ... NOTE
computeQScore: no visible global function definition for ‘terms’
Undefined global functions or variables:
terms
Consider adding
importFrom("stats", "terms")
to your NAMESPACE file.

CopilotAI
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ContributorAuthor
@copilot fix warning and note coming from workflows!

Check consistencies of the function arguments in the function code itself!
...
Fixed both issues in commit Fix R CMD check WARNING and NOTE:
  1. WARNING (plotZoomFovsMap.Rd undocumented args): Removed the unused csize and calpha parameters from the plotZoomFovsMap function signature — they were never used in the function body (equivalent arguments can be passed via ... to plotPolygons if needed).
  2. NOTE (computeQScore: no visible global function definition for 'terms'): Added terms to the @importFrom stats line in QC.R and added importFrom(stats,terms) to NAMESPACE.
@BenedettaBanzi
BenedettaBanzi
marked this pull request as ready for review
July 24, 2026 15:12
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Revision of qcscore_model_spe branch - #65
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Revision of qcscore_model_spe branch#65
drighelli with Copilot wants to merge 4 commits into
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CopilotAI
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  • Fixed some issues with QS computation with custom formula;
  • updated QC functions documentation;
  • added more customizable settings to plot functions;
  • function name standardization to Quality Score (QScore);
  • added backward-compatible deprecated wrappers for computeQCScore() and computeQCScoreFlags() following Bioconductor .Deprecated() guidelines;
  • updated vignettes.
CopilotAI
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[WIP] Revision of qcscore_model_spe branchRevision of qcscore_model_spe branchJul 24, 2026
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@copilot fix warning and note coming from workflows!

Check consistencies of the function arguments in the function code itself!
❯ checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'plotZoomFovsMap.Rd'
‘csize’ ‘calpha’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
❯ checking R code for possible problems ... NOTE
computeQScore: no visible global function definition for ‘terms’
Undefined global functions or variables:
terms
Consider adding
importFrom("stats", "terms")
to your NAMESPACE file.

CopilotAI
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ContributorAuthor
@copilot fix warning and note coming from workflows!

Check consistencies of the function arguments in the function code itself!
...
Fixed both issues in commit Fix R CMD check WARNING and NOTE:
  1. WARNING (plotZoomFovsMap.Rd undocumented args): Removed the unused csize and calpha parameters from the plotZoomFovsMap function signature — they were never used in the function body (equivalent arguments can be passed via ... to plotPolygons if needed).
  2. NOTE (computeQScore: no visible global function definition for 'terms'): Added terms to the @importFrom stats line in QC.R and added importFrom(stats,terms) to NAMESPACE.
@BenedettaBanzi
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marked this pull request as ready for review
July 24, 2026 15:12
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, 'i');
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Revision of qcscore_model_spe branch - #65
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drighelli with Copilot wants to merge 4 commits into
qscore_model_spefrom 
copilot/qcscore-model-spe
Open
Revision of qcscore_model_spe branch#65
drighelli with Copilot wants to merge 4 commits into
qscore_model_spefrom 
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CopilotAI
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  • Fixed some issues with QS computation with custom formula;
  • updated QC functions documentation;
  • added more customizable settings to plot functions;
  • function name standardization to Quality Score (QScore);
  • added backward-compatible deprecated wrappers for computeQCScore() and computeQCScoreFlags() following Bioconductor .Deprecated() guidelines;
  • updated vignettes.
CopilotAI
mentioned this pull request
Jul 24, 2026
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changed the title
[WIP] Revision of qcscore_model_spe branchRevision of qcscore_model_spe branchJul 24, 2026
CopilotAI
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from drighelliJuly 24, 2026 10:13
@drighelli
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@copilot fix warning and note coming from workflows!

Check consistencies of the function arguments in the function code itself!
❯ checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'plotZoomFovsMap.Rd'
‘csize’ ‘calpha’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
❯ checking R code for possible problems ... NOTE
computeQScore: no visible global function definition for ‘terms’
Undefined global functions or variables:
terms
Consider adding
importFrom("stats", "terms")
to your NAMESPACE file.

CopilotAI
commented
Jul 24, 2026

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ContributorAuthor
@copilot fix warning and note coming from workflows!

Check consistencies of the function arguments in the function code itself!
...
Fixed both issues in commit Fix R CMD check WARNING and NOTE:
  1. WARNING (plotZoomFovsMap.Rd undocumented args): Removed the unused csize and calpha parameters from the plotZoomFovsMap function signature — they were never used in the function body (equivalent arguments can be passed via ... to plotPolygons if needed).
  2. NOTE (computeQScore: no visible global function definition for 'terms'): Added terms to the @importFrom stats line in QC.R and added importFrom(stats,terms) to NAMESPACE.
@BenedettaBanzi
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marked this pull request as ready for review
July 24, 2026 15:12
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mentioned this pull request
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, 'i');
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Revision of qcscore_model_spe branch - #65
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drighelli with Copilot wants to merge 4 commits into
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copilot/qcscore-model-spe
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Revision of qcscore_model_spe branch#65
drighelli with Copilot wants to merge 4 commits into
qscore_model_spefrom 
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CopilotAI
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  • Fixed some issues with QS computation with custom formula;
  • updated QC functions documentation;
  • added more customizable settings to plot functions;
  • function name standardization to Quality Score (QScore);
  • added backward-compatible deprecated wrappers for computeQCScore() and computeQCScoreFlags() following Bioconductor .Deprecated() guidelines;
  • updated vignettes.
CopilotAI
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[WIP] Revision of qcscore_model_spe branchRevision of qcscore_model_spe branchJul 24, 2026
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@copilot fix warning and note coming from workflows!

Check consistencies of the function arguments in the function code itself!
❯ checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'plotZoomFovsMap.Rd'
‘csize’ ‘calpha’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
❯ checking R code for possible problems ... NOTE
computeQScore: no visible global function definition for ‘terms’
Undefined global functions or variables:
terms
Consider adding
importFrom("stats", "terms")
to your NAMESPACE file.

CopilotAI
commented
Jul 24, 2026

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ContributorAuthor
@copilot fix warning and note coming from workflows!

Check consistencies of the function arguments in the function code itself!
...
Fixed both issues in commit Fix R CMD check WARNING and NOTE:
  1. WARNING (plotZoomFovsMap.Rd undocumented args): Removed the unused csize and calpha parameters from the plotZoomFovsMap function signature — they were never used in the function body (equivalent arguments can be passed via ... to plotPolygons if needed).
  2. NOTE (computeQScore: no visible global function definition for 'terms'): Added terms to the @importFrom stats line in QC.R and added importFrom(stats,terms) to NAMESPACE.
@BenedettaBanzi
BenedettaBanzi
marked this pull request as ready for review
July 24, 2026 15:12
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Revision of qcscore_model_spe branch - #65
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Revision of qcscore_model_spe branch#65
drighelli with Copilot wants to merge 4 commits into
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CopilotAI
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  • Fixed some issues with QS computation with custom formula;
  • updated QC functions documentation;
  • added more customizable settings to plot functions;
  • function name standardization to Quality Score (QScore);
  • added backward-compatible deprecated wrappers for computeQCScore() and computeQCScoreFlags() following Bioconductor .Deprecated() guidelines;
  • updated vignettes.
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mentioned this pull request
Jul 24, 2026
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[WIP] Revision of qcscore_model_spe branchRevision of qcscore_model_spe branchJul 24, 2026
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from drighelliJuly 24, 2026 10:13
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@copilot fix warning and note coming from workflows!

Check consistencies of the function arguments in the function code itself!
❯ checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'plotZoomFovsMap.Rd'
‘csize’ ‘calpha’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
❯ checking R code for possible problems ... NOTE
computeQScore: no visible global function definition for ‘terms’
Undefined global functions or variables:
terms
Consider adding
importFrom("stats", "terms")
to your NAMESPACE file.

CopilotAI
commented
Jul 24, 2026

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ContributorAuthor
@copilot fix warning and note coming from workflows!

Check consistencies of the function arguments in the function code itself!
...
Fixed both issues in commit Fix R CMD check WARNING and NOTE:
  1. WARNING (plotZoomFovsMap.Rd undocumented args): Removed the unused csize and calpha parameters from the plotZoomFovsMap function signature — they were never used in the function body (equivalent arguments can be passed via ... to plotPolygons if needed).
  2. NOTE (computeQScore: no visible global function definition for 'terms'): Added terms to the @importFrom stats line in QC.R and added importFrom(stats,terms) to NAMESPACE.
@BenedettaBanzi
BenedettaBanzi
marked this pull request as ready for review
July 24, 2026 15:12
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mentioned this pull request
Jul 29, 2026
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Revision of qcscore_model_spe branch - #65
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drighelli with Copilot wants to merge 4 commits into
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copilot/qcscore-model-spe
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Revision of qcscore_model_spe branch#65
drighelli with Copilot wants to merge 4 commits into
qscore_model_spefrom 
copilot/qcscore-model-spe
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CopilotAI
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Jul 24, 2026•

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  • Fixed some issues with QS computation with custom formula;
  • updated QC functions documentation;
  • added more customizable settings to plot functions;
  • function name standardization to Quality Score (QScore);
  • added backward-compatible deprecated wrappers for computeQCScore() and computeQCScoreFlags() following Bioconductor .Deprecated() guidelines;
  • updated vignettes.
CopilotAI
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[WIP] Revision of qcscore_model_spe branchRevision of qcscore_model_spe branchJul 24, 2026
CopilotAI
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from drighelliJuly 24, 2026 10:13
@drighelli
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@copilot fix warning and note coming from workflows!

Check consistencies of the function arguments in the function code itself!
❯ checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'plotZoomFovsMap.Rd'
‘csize’ ‘calpha’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
❯ checking R code for possible problems ... NOTE
computeQScore: no visible global function definition for ‘terms’
Undefined global functions or variables:
terms
Consider adding
importFrom("stats", "terms")
to your NAMESPACE file.

CopilotAI
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@copilot fix warning and note coming from workflows!

Check consistencies of the function arguments in the function code itself!
...
Fixed both issues in commit Fix R CMD check WARNING and NOTE:
  1. WARNING (plotZoomFovsMap.Rd undocumented args): Removed the unused csize and calpha parameters from the plotZoomFovsMap function signature — they were never used in the function body (equivalent arguments can be passed via ... to plotPolygons if needed).
  2. NOTE (computeQScore: no visible global function definition for 'terms'): Added terms to the @importFrom stats line in QC.R and added importFrom(stats,terms) to NAMESPACE.
@BenedettaBanzi
BenedettaBanzi
marked this pull request as ready for review
July 24, 2026 15:12
@drighellidrighelli
mentioned this pull request
Jul 29, 2026
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Revision of qcscore_model_spe branch - #65
Open
drighelli with Copilot wants to merge 4 commits into
qscore_model_spefrom 
copilot/qcscore-model-spe
Open
Revision of qcscore_model_spe branch#65
drighelli with Copilot wants to merge 4 commits into
qscore_model_spefrom 
copilot/qcscore-model-spe
Conversation
CopilotAI
commented
Jul 24, 2026•

edited

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Contributor
  • Fixed some issues with QS computation with custom formula;
  • updated QC functions documentation;
  • added more customizable settings to plot functions;
  • function name standardization to Quality Score (QScore);
  • added backward-compatible deprecated wrappers for computeQCScore() and computeQCScoreFlags() following Bioconductor .Deprecated() guidelines;
  • updated vignettes.
CopilotAI
mentioned this pull request
Jul 24, 2026
 Merged

CopilotAI
changed the title
[WIP] Revision of qcscore_model_spe branchRevision of qcscore_model_spe branchJul 24, 2026
CopilotAI
requested a review
from drighelliJuly 24, 2026 10:13
@drighelli
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Jul 24, 2026

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@copilot fix warning and note coming from workflows!

Check consistencies of the function arguments in the function code itself!
❯ checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'plotZoomFovsMap.Rd'
‘csize’ ‘calpha’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
❯ checking R code for possible problems ... NOTE
computeQScore: no visible global function definition for ‘terms’
Undefined global functions or variables:
terms
Consider adding
importFrom("stats", "terms")
to your NAMESPACE file.

CopilotAI
commented
Jul 24, 2026

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ContributorAuthor
@copilot fix warning and note coming from workflows!

Check consistencies of the function arguments in the function code itself!
...
Fixed both issues in commit Fix R CMD check WARNING and NOTE:
  1. WARNING (plotZoomFovsMap.Rd undocumented args): Removed the unused csize and calpha parameters from the plotZoomFovsMap function signature — they were never used in the function body (equivalent arguments can be passed via ... to plotPolygons if needed).
  2. NOTE (computeQScore: no visible global function definition for 'terms'): Added terms to the @importFrom stats line in QC.R and added importFrom(stats,terms) to NAMESPACE.
@BenedettaBanzi
BenedettaBanzi
marked this pull request as ready for review
July 24, 2026 15:12
@drighellidrighelli
mentioned this pull request
Jul 29, 2026
 Merged

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