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Feature/mouse support #9

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Merged
shafighi merged 4 commits into from
Jun 2, 2026
Merged

Feature/mouse support #9

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5f50159
Add mouse (GRCm38) support: extended blacklisting and coverage metric
shafighi May 21, 2026
2f195ba
Add pericentromeric bin filter for mouse (GRCm38)
shafighi May 21, 2026
9e3a8d8
Add segmental duplication mask for mouse (GRCm38)
shafighi May 21, 2026
04fc71c
Replace mm9 replication timing source with mm10 liftover for mouse
shafighi May 21, 2026
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32 changes: 28 additions & 4 deletions R/core.R
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Original file line number Diff line number Diff line change
Expand Up @@ -759,9 +759,13 @@ readData <- function(bamfiles, binSize, species = "Human", filterChromosomes=c("
Biobase::pData(readCounts)["genome"] = genome
coverage = (readCounts@phenoData@data$used.reads * (as.numeric(isPaired) + 1) * read_size) / 3.2e9
Biobase::pData(readCounts)["coverage"] = coverage
} else if(species == "Mouse"){
Biobase::pData(readCounts)["genome"] = genome
coverage = (readCounts@phenoData@data$used.reads * (as.numeric(isPaired) + 1) * read_size) / 2.7e9
Biobase::pData(readCounts)["coverage"] = coverage
}
if(species == "Human" & extendedBlacklisting){

if(extendedBlacklisting & (species == "Human" | species == "Mouse")){
if(binSize < 10) stop("blacklisting doesn't support binsizes smaller than 10kb")
# this is because our blacklisted regions have a resolution of 10kb
if(binSize %in% c(200, 2000, 5000) && genome == "GRCh37"){
Expand Down Expand Up @@ -809,7 +813,9 @@ readData <- function(bamfiles, binSize, species = "Human", filterChromosomes=c("

if(species == "Human"){
Biobase::experimentData(readCounts)@other = list(species="Human", genome=genome)
}else{
} else if(species == "Mouse"){
Biobase::experimentData(readCounts)@other = list(species="Mouse", genome=genome)
} else {
Biobase::experimentData(readCounts)@other = list(species=species)
}

Expand All @@ -823,7 +829,7 @@ readData <- function(bamfiles, binSize, species = "Human", filterChromosomes=c("
#' @return QDNAseq object with updated bin usability
readFilter <- function(readCounts, genome="GRCh37"){

stopifnot(genome %in% c("GRCh37", "GRCh38"))
stopifnot(genome %in% c("GRCh37", "GRCh38", "GRCm38"))
if(genome == "GRCh37"){
gr = createGR(readCounts[,1,drop=FALSE])
excluded_regions_bed = readr::read_tsv(file.path(BASEDIR, "data/blacklisting/final_exclude_regions_hg19.bed"),
Expand All @@ -836,6 +842,24 @@ readFilter <- function(readCounts, genome="GRCh37"){
warning("blacklist has been optimized for GRCh37 only")
stop("Not supported")
}
if(genome == "GRCm38"){
gr = createGR(readCounts[,1,drop=FALSE])
valid_chrs = seqlevels(gr)
blacklist_bed = readr::read_tsv(file.path(BASEDIR, "data/blacklisting/mm10-blacklist.v2.bed"),
col_names = c("chromosome", "start", "end", "reason"), col_types="ciic")
pericentro_bed = readr::read_tsv(file.path(BASEDIR, "data/blacklisting/mm10_pericentromeric_exclude.bed"),
col_names = c("chromosome", "start", "end"), col_types="cii")
segdup_bed = readr::read_tsv(file.path(BASEDIR, "data/blacklisting/mm10_segdup.bed"),
col_names = c("chromosome", "start", "end"), col_types="cii")
excluded_regions_bed = dplyr::bind_rows(
blacklist_bed[, c("chromosome", "start", "end")],
pericentro_bed,
segdup_bed[segdup_bed$chromosome %in% valid_chrs, ]
)
excluded_regions = GRanges(seqnames=excluded_regions_bed$chromosome,
ranges = IRanges(start=excluded_regions_bed$start+1, end=excluded_regions_bed$end),
seqinfo = seqinfo(gr))
}

hits <- findOverlaps(excluded_regions, gr)

Expand Down
21 changes: 21 additions & 0 deletions data/blacklisting/mm10_pericentromeric_exclude.bed
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Original file line number Diff line number Diff line change
@@ -0,0 +1,21 @@
chr1 0 3000000
chr2 0 3000000
chr3 0 3000000
chr4 0 3000000
chr5 0 3000000
chr6 0 3000000
chr7 0 3000000
chr8 0 3000000
chr9 0 3000000
chr10 0 3000000
chr11 0 3000000
chr12 0 3000000
chr13 0 3000000
chr14 0 3000000
chr15 0 3000000
chr16 0 3000000
chr17 0 3000000
chr18 0 3000000
chr19 0 3000000
chrX 0 3000000
chrY 0 3000000
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