Error en .calculatePeakGeneCorrelations(GRN, TADs = TADs, knownLinks = knownLinks, : all(!is.na(map_peaks)) is not TRUE Además: Aviso: In normarg_seqnames2(seqnames, seqinfo) : levels in 'seqnames' with no entries in 'seqinfo' were dropped

[kbarrr]

Hello.

I am in the middle of GRaNIE tutorial and got this error:

GRN = addConnections_peak_gene(

• GRN, # El objeto GRN que contiene la información de los datos de RNA-seq y ATAC-seq
• overlapTypeGene = "TSS", # Usar TSS como referencia para la búsqueda de genes cercanos a los picos
• corMethod = "pearson", # Usar el coeficiente de correlación de Pearson
• promoterRange = 50000, # El rango de la vecindad en bp para correlacionar picos y genes
• TADs = NULL, # No se proporcionan TADs
• TADs_mergeOverlapping = FALSE, # No se usa este parámetro ya que no tienes TADs
• knownLinks = NULL, # No se utilizan enlaces conocidos
• knownLinks_separator = c(":", "-"), # Separadores para los enlaces conocidos (no utilizados)
• knownLinks_useExclusively = FALSE, # No se usan exclusivamente los enlaces conocidos
• shuffleRNACounts = TRUE, # Aleatorizar las etiquetas de RNA
• nCores = 2, # Usar 4 núcleos para el análisis
• plotDiagnosticPlots = TRUE, # Generar gráficos de diagnóstico
• plotGeneTypes = list(c("all"), c("protein_coding")), # Mostrar todos los tipos de genes y solo los codificantes
• outputFolder = NULL, # Usar el directorio de salida predeterminado
• forceRerun = TRUE # No forzar la ejecución si los resultados ya existen
• )
  INFO [2025-02-05 03:11:45]
  Preparing data

INFO [2025-02-05 03:11:45] Calculate peak gene overlaps based on either a fixed neighborhood size or defined TADs...
INFO [2025-02-05 03:11:45] Extend peaks based on user-defined extension size of 50000 up- and downstream.
INFO [2025-02-05 03:11:45] Finished successfully. Execution time: 0.2 secs
INFO [2025-02-05 03:11:45] Source distribution of peak-gene links:
INFO [2025-02-05 03:11:45] neighborhood: 73672
INFO [2025-02-05 03:11:45]
Finished preparing data

INFO [2025-02-05 03:11:45]
Calculate peak-gene correlations for real data

Error en .calculatePeakGeneCorrelations(GRN, TADs = TADs, knownLinks = knownLinks, :
all(!is.na(map_peaks)) is not TRUE
Además: Aviso:
In normarg_seqnames2(seqnames, seqinfo) :
levels in 'seqnames' with no entries in 'seqinfo' were dropped

GRN = addConnections_peak_gene(GRN, corMethod = "spearman", promoterRange = 10000,

•                            TADs = NULL, nCores = 1, plotDiagnosticPlots = T, plotGeneTypes = list(c("all")),
  

•                            forceRerun = TRUE)
  

INFO [2025-02-05 03:12:57]
Preparing data

INFO [2025-02-05 03:12:57] Calculate peak gene overlaps based on either a fixed neighborhood size or defined TADs...
INFO [2025-02-05 03:12:57] Extend peaks based on user-defined extension size of 10000 up- and downstream.
INFO [2025-02-05 03:12:58] Finished successfully. Execution time: 0.3 secs
INFO [2025-02-05 03:12:58] Source distribution of peak-gene links:
INFO [2025-02-05 03:12:58] neighborhood: 21510
INFO [2025-02-05 03:12:58]
Finished preparing data

INFO [2025-02-05 03:12:58]
Calculate peak-gene correlations for real data

Error en .calculatePeakGeneCorrelations(GRN, TADs = TADs, knownLinks = knownLinks, :
all(!is.na(map_peaks)) is not TRUE
Además: Aviso:
In normarg_seqnames2(seqnames, seqinfo) :
levels in 'seqnames' with no entries in 'seqinfo' were dropped

Would someone be able to assist me with this, please?

[lshep]

This is not a live location for opening issues. Please ask on support.bioconductor.org or as the package landing page suggests, bug reports and issues on the github repo https://git.embl.de/grp-zaugg/GRaNIE/issues