Error in initiate_grn() #70
Description
Dear developers,
I am getting a similar error message to #44 and hope you can help me fix it. I am following the quick start vignette as follows:
seurat
An object of class Seurat
370722 features across 18311 samples within 3 assays
Active assay: ATAC (303707 features, 288760 variable features)
2 layers present: counts, data
2 other assays present: RNA, SCT
5 dimensional reductions calculated: pca, umap_rna, lsi, umap_atac, umap
data("motifs")
seurat <- Seurat::FindVariableFeatures(seurat, assay = "RNA")
Finding variable features for layer counts
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
grn_object <- initiate_grn(seurat, rna_assay = "RNA", peak_assay = "ATAC")
Warning: Each of the 2 combined objects has sequence levels not in the other:
in 'x': GL000195.1, GL000205.2, GL000219.1, KI270711.1, KI270713.1, KI270721.1, KI270727.1, KI270728.1, KI270731.1
in 'y': chrMT
Make sure to always combine/compare objects based on the same reference
genome (use suppressWarnings() to suppress this warning).Warning: Each of the 2 combined objects has sequence levels not in the other:
in 'x': GL000195.1, GL000205.2, GL000219.1, KI270711.1, KI270713.1, KI270721.1, KI270727.1, KI270728.1, KI270731.1
in 'y': chrMT
Make sure to always combine/compare objects based on the same reference
genome (use suppressWarnings() to suppress this warning).Error in compatibleSeqnames(rep(seqnames(x), elementNROWS(y)), seqnames(y@unlistData)) :
Level set of 'x' must be subset of that of 'y', or vice versa
Then I tried the solution suggested above:
DefaultAssay(seurat) <- "ATAC"
granges(seurat)
main_chroms <- standardChromosomes(BSgenome.Hsapiens.UCSC.hg38)
keep_peaks <- as.logical(seqnames(granges(seurat)) %in% main_chroms)
seurat <- seurat[keep_peaks, ]
And got the following:
Error: None of the features provided found in this assay
Do you have any suggestions how to fix this? Thank you in advance!