TSSEnrichment() Errorin slot(object = object, name = layer) : argument "slot" is missing, with no default

[Sennyou]

Hello, I am trying to run Signac , but am running into the following error with the TSSEnrichment() function:

pbmc <- TSSEnrichment(object = pbmc, fast = FALSE, assay = "peaks")
Extracting TSS positions
Finding + strand cut sites
Finding - strand cut sites
Computing mean insertion frequency in flanking regions
Normalizing TSS score
Error in slot(object = object, name = layer) :
argument "slot" is missing, with no default

When I set fast=true, there is no problem. I tried for a long time but didn't find a solution. If you can help me, I will be very grateful.

Here is my code:

library(EnsDb.Hsapiens.v75)
library(patchwork)
library(Signac)
library(Seurat)
library(ggplot2)
library(hdf5r)
library(spatstat.geom)
library(biovizBase)

metadata <- read.csv(
file = "/atac_v1_pbmc_10k_singlecell.csv",
header = TRUE,
row.names = 1
)
counts <- Read10X_h5(filename = "/atac_v1_pbmc_10k_filtered_peak_bc_matrix.h5")

chrom_assay <- CreateChromatinAssay(
counts = counts,
sep = c(":", "-"),
genome = 'hg19',
fragments = '/atac_v1_pbmc_10k_fragments.tsv.gz',
min.cells = 10,
min.features = 200
)

pbmc <- CreateSeuratObject(
counts = chrom_assay,
assay = "peaks",
meta.data = metadata
)

pbmc <- TSSEnrichment(object = pbmc, fast = FALSE ,assay = "peaks")

The version:

packageVersion("Seurat")
[1] '5.0.1'
packageVersion("Signac")
[1] '1.12.0'
sessionInfo()
R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)

[timoast]

Hi @Sennyou, this should now be fixed on the develop branch. Please try with the updated version and see if you still have any issues:

remotes::install_github("stuart-lab/signac", ref="develop")

[Sennyou]

Thank you for your help. Following your method, the problem has been resolved. It means a lot to me.

[realmungmung]

Hi @Sennyou, this should now be fixed on the develop branch. Please try with the updated version and see if you still have any issues:

remotes::install_github("stuart-lab/signac", ref="develop")

Hello, I followed your suggestion but still got the same error. Should I install it in R or Rstudio?

[jgarces02]

Pretty obvious but once installed the development version, restart R. This worked for me.