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Zaugg Group
GRaNIE
Merge requests
!2
Return an error if consensus peaks overlap
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Return an error if consensus peaks overlap
overlapping-peak-fix
into
master
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Rim Moussa
requested to merge
overlapping-peak-fix
into
master
3 years ago
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df53e2d5
1 commit,
3 years ago
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src/GRNdev/R/core.R
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@@ -499,6 +499,20 @@ overlapPeaksAndTFBS <- function(GRN, nCores = 2, forceRerun = FALSE) {
# Construct GRanges
consensus.gr
=
.constructGRanges
(
GRN
@
data
$
peaks
$
consensusPeaks
,
seqlengths
=
seqlengths
,
genomeAssembly
)
consensus.gr.reduced
=
reduce
(
consensus.gr
)
# overlap the peaks
if
(
length
(
consensus.gr.reduced
)
<
length
(
consensus.gr
)){
message
=
paste0
(
"Overlapping peaks have been identified. This is not supported by the package."
)
# use the code below if you wish to return the peakIDs for the overlapping peaks:
# overlap.matrix = findOverlaps(setdiff(consensus.gr.reduced, consensus.gr), consensus.gr, maxgap=0) %>%
# mutate(filtered=TRUE) %>%
# spread(subjectHits, filtered, fill = FALSE)
# overlap.peakIDs = apply(overlap.matrix[,-1],1,function(x){return (paste(consensus.gr$peakID[unlist(x)], collapse=";"))})
.checkAndLogWarningsAndErrors
(
NULL
,
message
,
isWarning
=
FALSE
)
}
res.l
=
.execInParallelGen
(
nCores
,
returnAsList
=
TRUE
,
listNames
=
GRN
@
config
$
allTF
,
iteration
=
1
:
length
(
GRN
@
config
$
allTF
),
verbose
=
FALSE
,
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