No `graph` slot in GRaNIE object.
When loading an older object from a couple of months ago I get this non-critical error when just printing the object:
> x
Object of class: GRaNIE ( version 0.99.0 )
Data summary:
Number of peaks (filtered, all): 22188, 31449
Number of genes (filtered, all): 14463, 60620
Parameters:
Provided metadata:
name : Monocytes_R848
file_peaks : /g/scb/zaugg/kholmato/PROJECTS/Myeloid_ageing/ChIP/6.PeakCalling/stringent/consensusPeaks.minOverlap10.allBams.overlaps.bed.gz
file_rna : /g/scb/zaugg/kholmato/PROJECTS/Myeloid_ageing/RNA/6.GeneCounts/sampleSummary_singleEnd/geneCounts_beforeDuplicatesRemoval_clean_raw.tsv
file_sampleMetadata : /g/scb/zaugg/kholmato/PROJECTS/Myeloid_ageing/GRN/input/Sample_Metadata_Merged.tsv
genomeAssembly : hg38
Connections:
TF-peak links (1355 with FDR < 0.3)
peak-gene links (150103 with 250000 bp promoter range)
TF-peak-gene links (379 with TF-peak FDR 0.2 and peak-gene FDR NA)
Network-related:
Error in (new("standardGeneric", .Data = function (object) :
no slot of name "graph" for this object of class "GRN"
Maybe this should be handled without throwing the e-word, but some warning about package versions?