Hi,

I run into an error when I tried to use addLibraryFactors(qseaSet). Here is the full error message:

deriving TMM library factors for 66 samples
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'as.matrix': sequences chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY have incompatible genomes:
  - in 'x': hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38, hg38
  - in 'y': BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.h

and here is my codes

library(qsea)
library("GenomicRanges")
library("BSgenome.Hsapiens.UCSC.hg38")
library(tidyverse)
library(rtracklayer)
library("BiocParallel")

# build meta dataframe
# Define the directory containing the bam files
dir_path <- "/mnt/data/kfang/HuiZ/cfDNA/dedup_bam_pe"
# List all bam files in the directory
bam_files <- list.files(path = dir_path, pattern = "\\.bam$", full.names = TRUE)
bam_df <- tibble(file_name = bam_files) %>%
  # Extract the sample name from the filename
  mutate(sample_name = basename(file_name) %>%
           str_remove("_dedup.bam")) %>%
  # Filter out test files with 'T' in the sample name
  filter(!str_detect(sample_name, "_T")) %>%
  # Determine the tumor status based on the sample name
  mutate(group = if_else(str_detect(sample_name, "^OVC"), "cancer", "health"))
bam_df <- as.data.frame(bam_df)
bam_df$sex <- 'female'

# load Loyfer's region
dna_methy_regions <- import(con = '/home/kfang/data/kfang/HuiZ/cfDNA/GSE186458_blocks.s207.hg38.4bp.noM.bed', format = "BED")
dna_methy_regions <- trim(dna_methy_regions)
# load 
qseaSet=createQseaSet(sampleTable=bam_df, 
                      BSgenome="BSgenome.Hsapiens.UCSC.hg38", 
                      Regions = dna_methy_regions)

register(MulticoreParam(workers=10))
qseaSet=addCoverage(qseaSet, paired=TRUE, parallel=TRUE)
qseaSet=addCNV(qseaSet, file_name="file_name",window_size=3e6, 
               paired=TRUE, parallel=TRUE, MeDIP=TRUE)
qseaSet=addLibraryFactors(qseaSet)

I wondered if anyone could shed some light on it?

Best, Kun

genome(qseaSet@regions)<-"BSgenome.Hsapiens.UCSC.hg38" solve the problem