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Hello everyone, I am trying to run Pando on my dataset and I keep hitting this error:
grn <- infer_grn(grn,
+ peak_to_gene_method = 'Signac',
+ genes = grn@data@assays$SCT@var.features,
+ parallel = F,
+ tf_cor = 0.05,
+ method = "glm",
+ family = "gaussian",
+ scale = F,
+ verbose = T)
Selecting candidate regulatory regions near genes
Preparing model input
Fitting models for 2777 target genes
| | 0 % ~calculating
Error in str2lang(x) : <text>:1:10: unexpected input
1: wnt5b ~ 4_
^
I have tried multiple tutorials and methods including this, this and this
But in all of them, the same error came through. If someone can help me understand where and why this is coming, it would be really helpful
This is my current code:
library(JASPAR2020)
library(glmnet)
library(doParallel)
library(xgboost)
library(ggraph)
library(motifmatchr)
library(reshape2)
library(grr)
library(Pando)
library(TFBSTools)
grn <- initiate_grn(Control.data,
rna_assay = "SCT",
peak_assay = 'peaks',
exclude_exons = TRUE)
grn <- find_motifs(grn,
pfm = pwm_set,
motif_tfs = motif_tfs,
genome = BSgenome.Drerio.UCSC.danRer11)
grn@data@assays$peaks@annotation$gene_symbol=grn@data@assays$peaks@annotation$gene_name
grn@data@assays$ATAC@annotation$gene_name=grn@data@assays$ATAC@annotation$gene_id
library(doParallel)
registerDoParallel(1)
grn <- infer_grn(grn,
peak_to_gene_method = 'Signac',
genes = grn@data@assays$SCT@var.features,
parallel = F,
tf_cor = 0.05,
method = "glm",
family = "gaussian",
scale = F,
verbose = T)
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