filterpeaks error

[woooowonjin]

Hello, I'm a beginner in bioinformatics. I want to proceed with chromVAR using bulk ATAC-seq data, but I encountered an error. For the chromVAR input, I used 1) bam files and 2) peaks. For the peaks, I created a consensus peak file using the corceslab/ATAC_IterativeOverlapPeakMerging tool and inputted this file into the peaks. Everything seemed to work fine up to "Getting GC content of peaks." However, I encountered an error during the step counts_filtered <- filterPeaks(counts_filtered, non_overlapping = TRUE). The error was: "Matrix::rowSums(counts(object)) encountered the following error: object 'R_dense_rowSums' not found." Could you please help me solve this? Thank you.

#Loading the package

library(chromVAR)
library(motifmatchr)
library(Matrix)
library(SummarizedExperiment)
library(BiocParallel)
set.seed(2017)

#Setting multiprocessing options

register(SnowParam(workers = 4, type = "SOCK")) #Windiows

#Reading in inputs

#1)Peaks

peaks<- readRDS("iterative_2_0/All_Samples.fwp.filter.non_overlapping.rds")

head(peaks)
GRanges object with 6 ranges and 2 metadata columns:
seqnames ranges strand | score name
|
[1] chr1 827265-827765 * | 11.9715 2uM_1
[2] chr1 869700-870200 * | 15.9742 2uM_2
[3] chr1 904462-904962 * | 11.1568 2uM_3
[4] chr1 906688-907188 * | 15.3457 2uM_4
[5] chr1 911094-911594 * | 18.8817 2uM_5
[6] chr1 912767-913267 * | 22.2830 2uM_6

---

seqinfo: 93 sequences from an unspecified genome; no seqlengths

#peak sorting
peaks <- sort(peaks)

#2-Counts

bamfiles <- c(

• "bam/HepG2_0uM_D_sort_dedup.bam",
• "bam/HepG2_0uM_S_sort_dedup.bam",
• "bam/HepG2_0uM_W_sort_dedup.bam",
• "bam/HepG2_2uM_re1_sort_dedup.bam",
• "bam/HepG2_2uM_re2_sort_dedup.bam",
• "bam/HepG2_2uM_re3_sort_dedup.bam")

print(bamfiles)
[1] "bam/HepG2_0uM_D_sort_dedup.bam" "bam/HepG2_0uM_S_sort_dedup.bam" "bam/HepG2_0uM_W_sort_dedup.bam" "bam/HepG2_2uM_re1_sort_dedup.bam"
[5] "bam/HepG2_2uM_re2_sort_dedup.bam" "bam/HepG2_2uM_re3_sort_dedup.bam"

fragment_counts <- getCounts(bamfiles,

•                          peaks2, 
  

•                          paired = TRUE, 
  

•                          by_rg = FALSE, 
  

•                          format = "bam", 
  

•                          colData = DataFrame(condition = c("0uM", "0uM","0uM",
  

•                                                            "2uM", "2uM","2uM"), 
  

•                                              replicates = c("1", "2","3",
  

•                                                             "1", "2","3")))
  

Reading in file: bam/HepG2_0uM_D_sort_dedup.bam
Reading in file: bam/HepG2_0uM_S_sort_dedup.bam
Reading in file: bam/HepG2_0uM_W_sort_dedup.bam
Reading in file: bam/HepG2_2uM_re1_sort_dedup.bam
Reading in file: bam/HepG2_2uM_re2_sort_dedup.bam
Reading in file: bam/HepG2_2uM_re3_sort_dedup.bam

head(fragment_counts)
class: RangedSummarizedExperiment
dim: 6 6
metadata(0):
assays(1): counts
rownames: NULL
rowData names(2): score name
colnames(6): HepG2_0uM_D_sort_dedup.bam HepG2_0uM_S_sort_dedup.bam ... HepG2_2uM_re2_sort_dedup.bam HepG2_2uM_re3_sort_dedup.bam
colData names(3): condition replicates depth
#Getting GC content of peaks
library(BSgenome.Hsapiens.UCSC.hg38)

gc_counts <- addGCBias(fragment_counts,

•                         genome = BSgenome.Hsapiens.UCSC.hg38)
  

head(rowData(gc_counts))
DataFrame with 6 rows and 3 columns
score name bias

1 11.9715 2uM_1 0.694611
2 15.9742 2uM_2 0.736527
3 11.1568 2uM_3 0.746507
4 15.3457 2uM_4 0.608782
5 18.8817 2uM_5 0.610778
6 22.2830 2uM_6 0.612774

#Filtering inputs
counts_filtered <- filterPeaks(counts_filtered, non_overlapping = TRUE)
Matrix::rowSums(counts(object)) encountered the following error: object 'R_dense_rowSums' not found