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calculate_conservation = function(aln1, aln2, windowSize, which="1"){
## This function is used to calculate the conservation profiles for a pairwise alignment.
# x: a DNAStringSet with length 2 holds the alignment
# windowSize: the smooth window size
# which: which seq in the alignment is computed.
windowSize = as.integer(windowSize)
if(windowSize %% 2 == 0){
warning("windows size is not even, turned into odd by -1")
windowSize = windowSize - 1L
}
which = match.arg(which, c("1", "2"))
if(nchar(aln1) != nchar(aln2))
stop("'aln1' and 'aln2' must have the same number of characters")
if(which == "1"){
alignedSeq1 = aln1
alignedSeq2 = aln2
}else{
alignedSeq1 = aln2
alignedSeq2 = aln1
}
alignedSeq1 = strsplit(as.character(alignedSeq1), "")[[1]]
alignedSeq2 = strsplit(as.character(alignedSeq2), "")[[1]]
indexGap = alignedSeq1 == "-" | alignedSeq1 == "." | alignedSeq1 == "_"
alignedSeq1 = alignedSeq1[!indexGap]
alignedSeq2 = alignedSeq2[!indexGap]
matches = alignedSeq1 == alignedSeq2
conservations = runmean(matches, k=windowSize, alg="C", endrule="mean")
return(conservations)
}
setMethod("calConservation",
signature(aln1="DNAString", aln2="DNAString"),
function(aln1, aln2, windowSize=51L, which="1"){
calculate_conservation(as.character(aln1), as.character(aln2),
windowSize=windowSize, which=which)
}
)
setMethod("calConservation",
signature(aln1="DNAStringSet", aln2="missing"),
function(aln1, aln2, windowSize=51L, which="1"){
if(length(aln1) != 2)
stop("'aln1' must be of length 2 when 'aln2' is missing")
calculate_conservation(as.character(aln1[1]),
as.character(aln1[2]),
windowSize=windowSize, which=which)
}
)
setMethod("calConservation",
signature(aln1="character", aln2="missing"),
function(aln1, aln2, windowSize=51L, which="1"){
if(length(aln1) != 2)
stop("'aln1' must be of length 2 when 'aln2' is missing")
calculate_conservation(aln1[1], aln1[2],
windowSize=windowSize, which=which)
}
)
setMethod("calConservation",
signature(aln1="character", aln2="character"),
function(aln1, aln2, windowSize=51L, which="1"){
calculate_conservation(aln1, aln2,
windowSize=windowSize, which=which)
}
)
do_sitesearchOneStrand = function(pwm, aln1, aln2,
seqname1="Unknown1", seqname2="Unknown2",
strand, min.score,
conservation, cutoff, type="any"){
seq1 = gsub("(-|_|\\.)", "", aln1)
seq2 = gsub("(-|_|\\.)", "", aln2)
site1 = searchSeq(pwm, seq1, seqname=seqname1,
strand=strand, min.score=min.score)
site2 = searchSeq(pwm, seq2, seqname=seqname2,
strand=strand, min.score=min.score)
siteset1 = views(site1)
siteset2 = views(site2)
stopifnot(all(diff(start(siteset1)) >= 1) && all(diff(start(siteset2)) >= 1))
# not quite sure the views returned by matchPWM is ordered by start, just check here.
alignedSeq1 = strsplit(aln1, "")[[1]]
alignedSeq2 = strsplit(aln2, "")[[1]]
indexGap = alignedSeq1 == "-" | alignedSeq1 == "." | alignedSeq1 == "_"
seq12aln = seq_len(length(alignedSeq1))[!indexGap]
indexGap = alignedSeq2 == "-" | alignedSeq2 == "." | alignedSeq2 == "_"
seq22aln = seq_len(length(alignedSeq2))[!indexGap]
# If we only consider it matched when the starts match.
#pos1_in_aln = seq12aln[start(siteset1)]
#pos2_in_aln = seq22aln[start(siteset2)]
#matchedPairs = match(pos1_in_aln, pos2_in_aln)
ranges1_in_aln = IRanges(start=seq12aln[start(siteset1)],
end=seq12aln[end(siteset1)])
ranges2_in_aln = IRanges(start=seq22aln[start(siteset2)],
end=seq22aln[end(siteset2)])
matchedPairs = findLargestOverlaps(ranges1_in_aln, ranges2_in_aln)
## if no match, return empty ans_siteset
if(length(matchedPairs) == 0L){
return(list(ans_siteset1=site1[FALSE], ans_siteset2=site2[FALSE]))
}
# From now, we have matches
#conservations1 = mapply(window, start=start(siteset1),
# end=end(siteset1), MoreArgs=list(conservation),
# SIMPLIFY=FALSE)[!is.na(matchedPairs)]
conservations1 = mapply(window, start=start(siteset1),
end=end(siteset1), MoreArgs=list(conservation),
SIMPLIFY=FALSE)[queryHits(matchedPairs)]
if(type == "all"){
keep = sapply(lapply(conservations1, ">=", cutoff), all)
}else if(type == "any"){
keep = sapply(lapply(conservations1, ">=", cutoff), any)
}else{
stop(type, " is not supported yet!")
}
#ans_siteset1 = site1[!is.na(matchedPairs)][keep]
#ans_siteset2 = site2[na.omit(matchedPairs)][keep]
ans_siteset1 = site1[queryHits(matchedPairs)][keep]
ans_siteset2 = site2[subjectHits(matchedPairs)][keep]
return(list(ans_siteset1=ans_siteset1, ans_siteset2=ans_siteset2))
}
do_sitesearch = function(pwm, aln1, aln2,
seqname1="Unknown1", seqname2="Unknown2",
min.score, windowSize, cutoff,
strand="*", type="any", conservation){
# aln1, aln2: characters.
strand = match.arg(strand, c("+", "-", "*"))
type = match.arg(type, c("all", "any"))
if(nchar(aln1) != nchar(aln2))
stop("'aln1' and 'aln2' must have the same number of characters")
if(cutoff > 1 || cutoff < 0)
stop("cutoff must be from 0 to 1.")
if(is.null(conservation)){
conservations1 = calConservation(aln1, aln2,
windowSize=windowSize, which="1")
}else{
conservations1 = conservation
}
sitesetPos = NULL
sitesetNeg = NULL
if(strand %in% c("+", "*")){
sitesetPos = do_sitesearchOneStrand(pwm, aln1, aln2,
seqname1=seqname1, seqname2=seqname2,
strand="+", min.score=min.score,
conservation=conservations1,
cutoff=cutoff, type=type)
}
if(strand %in% c("-", "*")){
sitesetNeg = do_sitesearchOneStrand(pwm, aln1, aln2,
seqname1=seqname1, seqname2=seqname2,
strand="-", min.score=min.score,
conservation=conservations1,
cutoff=cutoff, type=type)
}
if(is.null(sitesetPos) && !is.null(sitesetNeg)){
ans_siteset1 <- sitesetNeg$ans_siteset1
ans_siteset2 <- sitesetNeg$ans_siteset2
}else if(!is.null(sitesetPos) && is.null(sitesetNeg)){
ans_siteset1 <- sitesetPos$ans_siteset1
ans_siteset2 <- sitesetPos$ans_siteset2
}else{
ans_siteset1 = do.call(c, list(sitesetPos$ans_siteset1,
sitesetNeg$ans_siteset1))
ans_siteset2 = do.call(c, list(sitesetPos$ans_siteset2,
sitesetNeg$ans_siteset2))
}
return(SitePairSet(siteset1=ans_siteset1, siteset2=ans_siteset2))
}
setMethod("doSiteSearch",
signature(aln1="character", aln2="character"),
function(pwm, aln1, aln2, min.score="80%",
windowSize=51L, cutoff=0.7,
conservation=NULL){
do_sitesearch(pwm, aln1, aln2, min.score=min.score,
windowSize=windowSize, cutoff=cutoff,
conservation=conservation)
}
)
setMethod("doSiteSearch",
signature(aln1="character", aln2="missing"),
function(pwm, aln1, aln2, min.score="80%",
windowSize=51L, cutoff=0.7,
conservation=NULL){
if(length(aln1) != 2)
stop("'aln1' must be of length 2 when 'aln2' is missing")
do_sitesearch(pwm, aln1[1], aln1[2], min.score=min.score,
windowSize=windowSize, cutoff=cutoff,
conservation=conservation)
}
)
setMethod("doSiteSearch",
signature(aln1="DNAStringSet", aln2="missing"),
function(pwm, aln1, aln2, min.score="80%",
windowSize=51L, cutoff=0.7,
conservation=NULL){
if(length(aln1) != 2)
stop("'aln1' must be of length 2 when 'aln2' is missing")
do_sitesearch(pwm, as.character(aln1[1]), as.character(aln1[2]),
min.score=min.score, windowSize=windowSize,
cutoff=cutoff, conservation=conservation)
}
)
setMethod("doSiteSearch",
signature(aln1="DNAString", aln2="DNAString"),
function(pwm, aln1, aln2, min.score="80%",
windowSize=51L, cutoff=0.7,
conservation=NULL){
do_sitesearch(pwm, as.character(aln1), as.character(aln2),
min.score=min.score, windowSize=windowSize,
cutoff=cutoff, conservation=conservation)
}
)
do_PairBSgenomeSearchPositive = function(pwm, BSgenome1, BSgenome2,
chr1, chr2,
min.score, chain){
## I know this is really stupid,
## but I am almost confused by the strand. So split ito positive and negative.
## search with Positive pwm
## BSgenome1, BSgenome2 are BSgenome object
## chr1, chr2 character
seq1 = getSeq(BSgenome1, chr1)
seq2 = getSeq(BSgenome2, chr2)
site1 = suppressWarnings(searchSeq(pwm, seq1,
seqname=chr1, strand="+",
min.score=min.score))
rm(seq1)
site1GRanges = GRanges(seqnames=chr1, ranges(site1@views), strand="+")
# we only care about the coordinate based on positive strand, only this coordinate is return by searchSeq.
site2GRanges = liftOver(site1GRanges, chain)
# reduce the ranges. can apply on a GRangesList!! Cool!
site2GRanges = reduce(site2GRanges)
lengths <- elementNROWS(site2GRanges)
site2GRanges = site2GRanges[lengths == 1L]
# so far, we drop the region with more ranges.
# Discuss with Boris for more details.
# only keep the ranges on chr2
site2GRanges = site2GRanges[as.character(seqnames(site2GRanges)) == chr2]
site1 = site1[as.integer(names(site2GRanges))]
# extend the ranges a bit. Let's use ncol of matrix
site2GRanges2 = GRanges(seqnames=as.character(seqnames(site2GRanges)),
ranges=IRanges(as.integer(start(site2GRanges)) -
ncol(pwm@profileMatrix),
as.integer(end(site2GRanges)) +
ncol(pwm@profileMatrix)
),
strand=as.character(strand(site2GRanges))
)
site2SeqsSet = getSeq(BSgenome2, site2GRanges2)
site2 = lapply(site2SeqsSet, function(seq1, pwm, min.score){
searchSeq(pwm, seq1, strand="+", min.score=min.score)
}, pwm, min.score)
lengths = sapply(site2, length)
site2 = site2[lengths > 0L]
site1 = site1[lengths > 0L]
if(length(site2) == 0L){
site2 = site1
return(list(site1=site1, site2=site2))
}
site2 = do.call(c, site2)
site2GRanges2 = site2GRanges2[lengths > 0L]
# correct the ranges in site2 for negative strand.
lengthChr2 = length(seq2)
indexNegative = as.logical(strand(site2GRanges2) == "-")
ranges(site2GRanges2)[indexNegative] =
IRanges(start=lengthChr2-end(site2GRanges2)[indexNegative]+1,
end=lengthChr2-start(site2GRanges2)[indexNegative]+1
)
# build a new site2 with chr2 as subject and new ranges.
ans_site2 =
SiteSet(
views=Views(subject=seq2,
start=start(views(site2)) + start(site2GRanges2) - 1,
end=end(views(site2)) + start(site2GRanges2) - 1
),
seqname=chr2,
score=score(site2),
strand=as.character(strand(site2GRanges2)),
sitesource="TFBS", primary="TF binding site",
pattern=pwm
)
# correct the strand in site2, some are "-" after liftover
return(list(site1=site1, site2=ans_site2))
}
do_PairBSgenomeSearchNegative = function(pwm, BSgenome1, BSgenome2,
chr1, chr2,
min.score, chain){
## deal with the negative strand
seq1 = getSeq(BSgenome1, chr1)
seq2 = getSeq(BSgenome2, chr2)
site1 = suppressWarnings(searchSeq(pwm, seq1,
seqname=chr1, strand="-",
min.score=min.score))
rm(seq1)
site1GRanges = GRanges(seqnames=chr1, ranges(site1@views), strand="+")
site2GRanges = liftOver(site1GRanges, chain)
site2GRanges = reduce(site2GRanges)
lengths = sapply(site2GRanges, length)
site2GRanges = site2GRanges[lengths == 1L]
site2GRanges = site2GRanges[as.character(seqnames(site2GRanges)) == chr2]
site1 = site1[as.integer(names(site2GRanges))]
site2GRanges2 =
GRanges(seqnames=as.character(seqnames(site2GRanges)),
ranges=IRanges(as.integer(start(site2GRanges)) -
ncol(pwm@profileMatrix),
as.integer(end(site2GRanges)) +
ncol(pwm@profileMatrix)
),
strand=as.character(strand(site2GRanges))
)
site2SeqsSet = getSeq(BSgenome2, site2GRanges2)
site2 = lapply(site2SeqsSet, function(seq1, pwm, min.score){
searchSeq(pwm, seq1, strand="-", min.score=min.score)
}, pwm, min.score)
lengths = sapply(site2, length)
site2 = site2[lengths > 0L]
site1 = site1[lengths > 0L]
if(length(site2) == 0L){
site2 = site1
return(list(site1=site1, site2=site2))
}
site2 = do.call(c, site2)
site2GRanges2 = site2GRanges2[lengths > 0L]
# correct the ranges in site2 for negative strand.
lengthChr2 = length(seq2)
indexNegative = as.logical(strand(site2GRanges2) == "-")
ranges(site2GRanges2)[indexNegative] =
IRanges(start=lengthChr2-end(site2GRanges2)[indexNegative]+1,
end=lengthChr2-start(site2GRanges2)[indexNegative]+1
)
# build a new site2 with chr2 as subject and new ranges.
ans_site2 =
SiteSet(
views=Views(subject=seq2,
start=start(views(site2)) + start(site2GRanges2) - 1,
end=end(views(site2)) + start(site2GRanges2) - 1
),
seqname=chr2,
score=score(site2),
strand=chartr("+-", "-+", as.character(strand(site2GRanges2))),
sitesource="TFBS", primary="TF binding site",
pattern=pwm
)
return(list(site1=site1, site2=ans_site2))
}
do_PairBSgenomeSearchNew <- function(pwm, BSgenome1, BSgenome2,
chr1, chr2,
min.score, chain,
strand){
## I know this is really stupid,
## but I am almost confused by the strand. So split ito positive and negative.
## search with Positive pwm
## BSgenome1, BSgenome2 are BSgenome object
## chr1, chr2 character
seq1 <- getSeq(BSgenome1, chr1)
seq2 <- getSeq(BSgenome2, chr2)
site1 <- suppressWarnings(searchSeq(pwm, seq1,
seqname=chr1, strand=strand,
min.score=min.score))
rm(seq1)
site2 <- suppressWarnings(searchSeq(pwm, seq2,
seqname=chr2, strand=strand,
min.score=min.score))
rm(seq2)
site1GRanges <- GRanges(seqnames=chr1, ranges(site1@views), strand="+")
site2GRanges <- GRanges(seqnames=chr2, ranges(site2@views), strand="+")
# we only care about the coordinate based on positive strand,
# only this coordinate is return by searchSeq.
site2GRangesLift <- liftOver(site1GRanges, chain)
# reduce the ranges. can apply on a GRangesList!! Cool!
site2GRangesLift <- reduce(site2GRangesLift)
lengths <- elementNROWS(site2GRangesLift)
indexLength1 <- which(lengths == 1L)
site2GRangesLift <- site2GRangesLift[indexLength1]
# so far, we drop the region with more ranges.
# Discuss with Boris for more details.
# only keep the ranges on chr2
site2GRangesLift <- unlist(site2GRangesLift)
indexForChr <- which(seqnames(site2GRangesLift) == chr2)
site2GRangesLift <- site2GRangesLift[indexForChr]
indexToKeepSite1 <- indexLength1[indexForChr]
# extend the ranges a bit. Let's use ncol of matrix
site2GRangesLiftMerged <-
GRanges(seqnames=seqnames(site2GRangesLift),
ranges=IRanges(start(site2GRangesLift) -
ncol(pwm@profileMatrix),
end(site2GRangesLift) +
ncol(pwm@profileMatrix)
),
strand=strand(site2GRangesLift)
)
# Let's see how site2GRangesLiftMerged overlaps with site2GRanges
hits <- findOverlaps(site2GRangesLiftMerged, site2GRanges, ignore.strand=TRUE)
indexToKeepSite1 <- indexToKeepSite1[queryHits(hits)]
indexToKeepSite2 <- subjectHits(hits)
return(list(site1=site1[indexToKeepSite1], site2=site2[indexToKeepSite2]))
}
do_PairBSgenomeSearch = function(pwm, BSgenome1, BSgenome2, chr1, chr2,
strand, min.score, chain){
strand = match.arg(strand, c("+", "-", "*"))
sitesetPos = NULL
sitesetNeg = NULL
if(strand %in% c("+", "*")){
sitesetPos =
do_PairBSgenomeSearchNew(pwm, BSgenome1, BSgenome2,
chr1, chr2, min.score, chain,
strand="+")
}
if(strand %in% c("-", "*")){
sitesetNeg =
do_PairBSgenomeSearchNew(pwm, BSgenome1, BSgenome2,
chr1, chr2, min.score, chain,
strand="-")
}
ans_siteset1 = do.call(c, list(sitesetPos$site1, sitesetNeg$site1))
ans_siteset2 = do.call(c, list(sitesetPos$site2, sitesetNeg$site2))
return(SitePairSet(siteset1=ans_siteset1, siteset2=ans_siteset2))
}
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