satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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`CreateMotifMatrix` Error in fixupDN.if.valid(value, x@Dim) : length of Dimnames[[1]] (1) is not equal to Dim[1] (0) #9204

Closed danli349 closed 3 months ago

danli349 commented 3 months ago

Hello:

When run CreateMotifMatrix:

library(chromVAR)
library(JASPAR2020)
library(TFBSTools)
library(motifmatchr)
library(BSgenome.Mmusculus.UCSC.mm10)

DefaultAssay(pbmc) <- "ATAC"
pwm_set <- getMatrixSet(x = JASPAR2020, opts = list(species = 10090, all_versions = FALSE))
motif.matrix <- CreateMotifMatrix(features = granges(pbmc), pwm = pwm_set, genome = 'mm10', use.counts = FALSE)

How can I solve this error?

R[write to console]: Warning in CreateMotifMatrix(features = granges(pbmc), pwm = pwm_set, genome = "mm10",  :
R[write to console]: 

R[write to console]:  Not all seqlevels present in supplied genome

R[write to console]: Error in fixupDN.if.valid(value, x@Dim) : 
  length of Dimnames[[1]] (1) is not equal to Dim[1] (0)

R[write to console]: In addition: 
R[write to console]: Warning message:

R[write to console]: In .merge_two_Seqinfo_objects(x, y) :
R[write to console]: 

R[write to console]:  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)

Error in fixupDN.if.valid(value, x@Dim) : 
  length of Dimnames[[1]] (1) is not equal to Dim[1] (0)

Thanks

longmanz commented 3 months ago

Hi, Thank you for using Signac. Please post your issue at https://github.com/stuart-lab/signac/issues .