Error filtering the sample

[Chhiring-Lama]

Hi, I am using Cellranger output to create the SummarizedExperiment object for chromvar. Instead of using the bam/bed file (as it was not working), I used the count and peakranges from a chromatin assay from seurat to create the object and it seems to work. However, when I try filtering the low reads from the sample I get the following error:

Error in filterSamples(fragment_counts) : colData for object must have column named depth with total reads per sample

Is there a function to add depth to the object@coldata?

This is my code:

#create a chromatin assay for these specific peaks
granges_pax5_pos_peaks <- StringToGRanges(PAX5_positive_peaks)

##create new count matrix based on the peaks above
macs2_counts_peaks <- FeatureMatrix(
fragments = Fragments(bm_1121_int),
features = granges_pax5_pos_peaks,
cells = colnames(bm_1121_int)
)

##subset the atac assay to only include the above peaks
peak_counts <- CreateChromatinAssay(
counts = macs2_counts_peaks,
fragments = "atac_fragments.tsv.gz",
annotation = annotation
)

create summarized experiment

fragment_counts <- SummarizedExperiment(assays = list(counts = peak_counts@counts),
rowRanges = peak_counts@ranges)

#Computes GC content for peaks
fragment_counts <- addGCBias(fragment_counts, genome = BSgenome.Hsapiens.UCSC.hg38)

counts_filtered <- filterSamples(fragment_counts)

-----error------
Error in filterSamples(fragment_counts) :
colData for object must have column named depth with total reads per sample