Develop olly by ococrook · Pull Request #46 · ococrook/hdxstats

ococrook · 2026-01-30T13:28:49Z

No description provided.

Copilot

Pull request overview

This pull request adds a new comprehensive vignette demonstrating the analysis of SecA protein hydrogen deuterium exchange mass spectrometry data, along with important bug fixes and code improvements in the hdxstats package.

Changes:

Added a new case study vignette showing complete HDX-MS analysis workflow for SecA protein data
Fixed critical bug in forestPlot function where model2 parameters were incorrectly assigned from model1
Improved forestPlot function to return plot object instead of printing it
Updated package metadata including version bump (1.0 → 1.0.1) and corrected Authors@R format
Enhanced class flexibility by changing vis slot type from "gg" to "ANY"
Added new imports to NAMESPACE and DESCRIPTION

Reviewed changes

Copilot reviewed 6 out of 9 changed files in this pull request and generated 14 comments.

Show a summary per file

File	Description
vignettes/hdxstats-secA-casestudy.Rmd	New comprehensive vignette demonstrating HDX-MS analysis workflow on SecA protein data with functional data analysis approaches
R/hdxstat-methods.R	Modified `coef` method to handle edge case when output has only 1 row by transposing the result
R/hdxstat-class.R	Changed `vis` slot type from "gg" to "ANY" to allow more flexible data storage
R/functionalAnalysis-plots.R	Fixed bug using model1 instead of model2, and changed from print to return for better API design
NAMESPACE	Added new imports for longFormat, brewer.pal, is, and several packages via import()
DESCRIPTION	Updated version to 1.0.1, corrected Authors@R format, expanded description, and added stats to imports

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

Copilot · 2026-01-30T13:34:12Z

+              if(dim(.out)[1] == 1){
+                  nm <- colnames(.out)[1]
+                  .out <- t(.out)
+                  colnames(.out) <- nm
+              }
              rownames(.out) <- c("null", paste0("alt", seq.int(length(object))))


The logic for preserving column names appears incorrect. When transposing a matrix with 1 row, you're saving only the first column name, but after transposing, you should preserve all the original column names as the new row names, not just the first one. Consider saving the entire colnames(.out) vector before transposing, then assigning it as rownames after the transpose.

Suggested change

if(dim(.out)[1] == 1){

nm <- colnames(.out)[1]

.out <- t(.out)

colnames(.out) <- nm

}

rownames(.out) <- c("null", paste0("alt", seq.int(length(object))))

if (dim(.out)[1] == 1) {

## Preserve all original column names as row names after transposing

nm <- colnames(.out)

.out <- t(.out)

rownames(.out) <- nm

} else {

rownames(.out) <- c("null", paste0("alt", seq.int(length(object))))

}

Copilot · 2026-01-30T13:34:12Z

+
+# Introduction
+
+Ahdash et al. performed HDX-MS on the baceterial sec translocon, a multi-protein


Spelling error: 'baceterial' should be 'bacterial'.

Suggested change

Ahdash et al. performed HDX-MS on the baceterial sec translocon, a multi-protein

Ahdash et al. performed HDX-MS on the bacterial sec translocon, a multi-protein

Copilot · 2026-01-30T13:34:12Z

+
+The data is stored as a .csv, we need to covert it to an object of class
+`QFeatures`. This is performed in a number of steps which we detail below. The
+data is contained within the package and so can be loaded by specificy 


Spelling error: 'specificy' should be 'specifying'.

Suggested change

data is contained within the package and so can be loaded by specificy

data is contained within the package and so can be loaded by specifying

Copilot · 2026-01-30T13:34:12Z

+
+```
+
+We an use a forest plot to examine the differneces


Grammar error: 'We an use' should be 'We can use'.

Suggested change

We an use a forest plot to examine the differneces

We can use a forest plot to examine the differneces

Copilot · 2026-01-30T13:34:13Z

+vignette: |
+  %\VignetteIndexEntry{SecA hydrogen deuterium exchange mass spectrometry data}
+  %\VignetteEngine{knitr::rmarkdown}
+  %%\VignetteKeywords{Mass Spectrometry, MS, MSMS, Proteomics, Metabolomics, Infrastructure, Quantitative} %\VignetteEncoding{UTF-8}


The vignette metadata has a formatting issue. The VignetteKeywords and VignetteEncoding directives are on the same line. They should be on separate lines for proper parsing. Additionally, there's a double percent sign (%%) before VignetteKeywords which should be a single percent sign (%).

Suggested change

%%\VignetteKeywords{Mass Spectrometry, MS, MSMS, Proteomics, Metabolomics, Infrastructure, Quantitative} %\VignetteEncoding{UTF-8}

%\VignetteKeywords{Mass Spectrometry, MS, MSMS, Proteomics, Metabolomics, Infrastructure, Quantitative}

%\VignetteEncoding{UTF-8}

Copilot · 2026-01-30T13:34:14Z

+
+```{r, fig.width= 22, fig.height = 15}
+#We need to provide an indication of "difference" so we can examine deprotected
+# or prected regions


Spelling error: 'prected' should be 'protected'.

Suggested change

# or prected regions

# or protected regions

Copilot · 2026-01-30T13:34:14Z

+		                comment = c(ORCID = "0000-0001-5669-8506"),
+		                role = c("aut", "cre")))
 Description: The hdxstats package enables the analysis and visualisation
    of hydrogen deuterium exchange mass spectromery experiments. It supports


Spelling error: 'spectromery' should be 'spectrometry'.

Suggested change

of hydrogen deuterium exchange mass spectromery experiments. It supports

of hydrogen deuterium exchange mass spectrometry experiments. It supports

Copilot · 2026-01-30T13:34:14Z

+    toc_float: yes
+abstract: "This vignette describes how to analyse a mass-spectrometry based  hydrogen
+  deuterium exchange experiment, in particular we focus on empirical Bayes functional
+  models and visualisations. This vignette descibes a case-study for analysing


Spelling error: 'descibes' should be 'describes'.

Suggested change

models and visualisations. This vignette descibes a case-study for analysing

models and visualisations. This vignette describes a case-study for analysing

Copilot · 2026-01-30T13:34:15Z

+membrane. Here we analyse this experiment using our functional data analysis
+approaches
+
+# loading packges


Spelling error: 'packges' should be 'packages'.

Suggested change

# loading packges

# loading packages

Copilot · 2026-01-30T13:34:15Z

+
+```
+
+We an use a forest plot to examine the differneces


Spelling error: 'differneces' should be 'differences'.

Suggested change

We an use a forest plot to examine the differneces

We an use a forest plot to examine the differences

ococrook and others added 12 commits February 15, 2022 10:34

add secA data

d1bca65

fix typo in forest plot

572dae7

new case study

5e83a1f

smll change to case study

33534a5

fix namespace

c942862

small fix

771d4cf

swapped print with return in foresplot function

6c6acb8

Update hdxstat-class.R

20d69ce

Update hdxstat-class.R

a8de7ae

Change vis slot type to ANY in HdxStatModel

457f63a

Update DESCRIPTION

c1f2400

Bump version from 0.99.1 to 1.0.1

d0dd4e0

ococrook requested a review from Copilot January 30, 2026 13:28

Copilot started reviewing on behalf of ococrook January 30, 2026 13:29 View session

Copilot AI reviewed Jan 30, 2026

View reviewed changes

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Develop olly#46

Develop olly#46
ococrook wants to merge 12 commits intomainfrom
developOlly

ococrook commented Jan 30, 2026

Uh oh!

Copilot AI left a comment

Uh oh!

Copilot AI Jan 30, 2026

Uh oh!

Copilot AI Jan 30, 2026

Uh oh!

Copilot AI Jan 30, 2026

Uh oh!

Copilot AI Jan 30, 2026

Uh oh!

Copilot AI Jan 30, 2026

Uh oh!

Copilot AI Jan 30, 2026

Uh oh!

Copilot AI Jan 30, 2026

Uh oh!

Copilot AI Jan 30, 2026

Uh oh!

Copilot AI Jan 30, 2026

Uh oh!

Copilot AI Jan 30, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants


		# Introduction

		Ahdash et al. performed HDX-MS on the baceterial sec translocon, a multi-protein

	data is contained within the package and so can be loaded by specificy
	data is contained within the package and so can be loaded by specifying

	We an use a forest plot to examine the differneces
	We can use a forest plot to examine the differneces

	%%\VignetteKeywords{Mass Spectrometry, MS, MSMS, Proteomics, Metabolomics, Infrastructure, Quantitative} %\VignetteEncoding{UTF-8}
	%\VignetteKeywords{Mass Spectrometry, MS, MSMS, Proteomics, Metabolomics, Infrastructure, Quantitative}
	%\VignetteEncoding{UTF-8}

	of hydrogen deuterium exchange mass spectromery experiments. It supports
	of hydrogen deuterium exchange mass spectrometry experiments. It supports

	models and visualisations. This vignette descibes a case-study for analysing
	models and visualisations. This vignette describes a case-study for analysing

Conversation

ococrook commented Jan 30, 2026

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Reviewed changes

Uh oh!

Copilot AI Jan 30, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 30, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 30, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 30, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 30, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 30, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 30, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 30, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 30, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Jan 30, 2026

Choose a reason for hiding this comment

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants