Bioc3.19

[maddygriz]

• Seurat v5 coercions, resolves Prepare for upcoming Seurat v5 release #190, resolves Error coercing GeoMx data to Seurat object #191
• improved proteogenomics error handling
• bug fix on area filtering
• old PKC compatibility, resolves Handle older assay IDs #185

devtools::check()

warning = qpdf

R CMD build --keep-empty-dirs --no-resave-data GeomxTools & R CMD check

• checking PDF version of manual ... WARNING
• checking PDF version of manual without index ... ERROR

[maddygriz]

IPA test data can be found at HSDATA\SABonnett\GeoMx Tools\IPA Test

devtools::check()
0 errors ✔ | 1 warning ✖ | 6 notes ✖
❯ checking for unstated dependencies in examples ... OK
WARNING
‘qpdf’ is needed for checks on size reduction of PDFs

R CMD build --keep-empty-dirs --no-resave-data GeomxTools & R CMD check
Status: 1 ERROR, 1 WARNING, 5 NOTEs

• checking PDF version of manual ... WARNING
• checking PDF version of manual without index ... ERROR

[NicoleEO]

@maddygriz there seems to be an issue with readPKC getting gene id from IPA pkc. Also, is there any chance to add RTSID to featureData as well? It was also found that the fig() function was not working, but may be related to the GeneID missing from featureData after readPKC issue.

[maddygriz]

@mgrout81 Dave H found an issue on this branch about pkc info not being added to the feature metadata correctly. I have addressed that issue.

[mgrout81]

Thanks, I will update my package accordingly.

[mgrout81]

readPKCFile() appears to be working as expected. NA values above are in negative probes.

[maddygriz]

Megan approved and completed PR