buildGraph error

[yangjie4546]

Describe the bug
When I run buildGraph function in R, with the imported data "pbmc_small", some error happened "Error in x[, seq_len(d)] : subscript out of bounds". Is miloR::buildGraph is not suitable for seurat v4?

Hope for your reply,thank you.

## your code

library(Seurat)
data("pbmc_small")
pbmc_small_sce <- as.SingleCellExperiment(pbmc_small)
pbmc_small_milo <- Milo(pbmc_small_sce)
miloR::buildGraph(pbmc_small_milo,k=10,d=30)

Full error traceback
Error in x[, seq_len(d)] : subscript out of bounds

[yangjie4546]

Describe the bug When I run buildGraph function in R, with the imported data "pbmc_small", some error happened "Error in x[, seq_len(d)] : subscript out of bounds". Is miloR::buildGraph is not suitable for seurat v4?

Hope for your reply,thank you.

## your code

library(Seurat)
data("pbmc_small")
pbmc_small_sce <- as.SingleCellExperiment(pbmc_small)
pbmc_small_milo <- Milo(pbmc_small_sce)
miloR::buildGraph(pbmc_small_milo,k=10,d=30)

Full error traceback Error in x[, seq_len(d)] : subscript out of bounds

By the way, I don't want to update the seurat package totally because we have analysed the data based on V4 of seurat package.

[MikeDMorgan]

Hi @yangjie4546 Please post (1) the full traceback, and (2) the output of your sessionInfo()

[yangjie4546]

Hi @yangjie4546 Please post (1) the full traceback, and (2) the output of your sessionInfo()

##the full traceback:
library(Seurat)
data("pbmc_small")
pbmc_small_sce <- as.SingleCellExperiment(pbmc_small)
pbmc_small_milo <- Milo(pbmc_small_sce)
miloR::buildGraph(pbmc_small_milo,k=10,d=30)

##sessionLnfo()
Error in x[, seq_len(d)] : subscript out of bounds

[MikeDMorgan]

Hi @yangjie4546 Please post (1) the full traceback, and (2) the output of your sessionInfo()

[yangjie4546]

Hi I have solved the problem by amending the parameter including k and d.
Thanks!