Hi, I am trying to use the RP model to generate the gene activity score to 10x scATAC data. I installed MAESTRO R version as well as python version and setup reticulate. Yet, it is still throwing errors as follows. Do you have a suggestion?
# python related
library(reticulate)
use_python("/path/to/python", required = TRUE)
obj.gene <- ATACCalculateGenescore(obj,
organism = "GRCh38",
decaydistance = 10000,
model = "Enhanced")
output
Error in as.integer(as_r_value(x$indices)): cannot coerce type 'environment' to vector of type 'integer'
Traceback:
1. ATACCalculateGenescore(obj, organism = "GRCh38", decaydistance = 10000,
. model = "Enhanced")
2. calculate_RP_score(cell_peaks = inputMat, peaks_list = peaks_list,
. gene_bed_df = refgenes.genescore, genes_list = NULL, decay = decaydistance,
. model = model)
3. py_to_r(result)
4. py_to_r.python.builtin.tuple(result)
5. lapply(converted, function(object) {
. if (inherits(object, "python.builtin.object"))
. py_to_r(object)
. else object
. })
6. FUN(X[[i]], ...)
7. py_to_r(object)
8. py_to_r.scipy.sparse.csc.csc_matrix(object)
9. new("dgCMatrix", i = as.integer(as_r_value(x$indices)), p = as.integer(as_r_value(x$indptr)),
. x = as.vector(as_r_value(x$data)), Dim = as.integer(dim(x)))
10. initialize(value, ...)
11. initialize(value, ...)
12. callNextMethod()
13. .nextMethod(.Object = .Object, ... = ...)
hoondy
commented
3 years ago
Hi, I am trying to use the RP model to generate the gene activity score to 10x scATAC data. I installed MAESTRO R version as well as python version and setup reticulate. Yet, it is still throwing errors as follows. Do you have a suggestion?
output
session info