Getting first or last hit from a Hits object
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Peter Hickey ▴ 630
@petehaitch
Last seen 29 days ago
Walter and Eliza Hall Institute of Mediā€¦
Hi all, Suppose I've created a Hits object by all_hits <- findOverlaps(query, subject, select = 'all', type = 'any') and now I want to get the first (or last) hit for each query. Of course, I could use first_hits <- findOverlaps(query, subject, select = 'first', type = 'any') last_hits <- findOverlaps(query, subject, select = 'last', type = 'any') but I this isn't necessary as all the required information is in the all_hits Hits object. I was unable to find a function to do what I wanted, however, based at the source for findOverlaps-methods.R (actually Hector's branch at https://github.com/hcorrada/GenomicRanges/blob/master/R/findOverlaps- methods.R) I wrote the following simple functions getFirstHit <- function(all_hits){ ans <- rep.int(NA_integer_, queryLength(all_hits)) oo <- IRanges:::orderIntegerPairs(queryHits(all_hits), subjectHits(all_hits), decreasing = TRUE) ans[queryHits(all_hits)[oo]] <- subjectHits(all_hits)[oo] return(ans) } getLastHit <- function(all_hits){ ans <- rep.int(NA_integer_, queryLength(all_hits)) ans[queryHits(all_hits)] <- subjectHits(all_hits) return(ans) } These do what I want and are faster than re-running findOverlaps for my use case (millions of query intervals with tens of thousands of subject intervals) Now to my questions: (1) Did I just overlook built-in "getFirstHit" and "getLastHit" functions? (2) Would others find "getFirstHit" and "getLastHit" useful enough to justify their inclusion in GenomicRanges (or IRanges, wherever it belongs)? (3) I recall some discussion on this mailing list and Rdevel stating that using ":::" to access non-exported functions isn't a great idea for use in package code. If I need to include my own "getFirstHit" would someone be so kind as to point me to the best advice for avoiding calls to ":::" in my code to access IRanges:::orderIntegerPairs(queryHits)? Many thanks, Pete -------------------------------- Peter Hickey, PhD Student/Research Assistant, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Vic 3052, Australia. Ph: +613 9345 2324 hickey@wehi.edu.au http://www.wehi.edu.au ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:8}}
IRanges GenomicRanges IRanges GenomicRanges • 1.3k views
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@harris-a-jaffee-3972
Last seen 8.3 years ago
United States
I needed essentially your "last_hits" for bumphunter:::fuzzy.match2 In your notation, it comes out: last_hits_rows <- cumsum(rle(queryHits(all_hits))$lengths) last_hits <- all_hits[last_hits_rows,] Having expended that effort, you could do first_hits_rows <- c(1, 1 + last_hits_rows[-length(query)]) Maybe there's a better way. I have not compared these to anything of Hector's. On Oct 20, 2013, at 4:32 PM, Peter Hickey <hickey at="" wehi.edu.au=""> wrote: > Hi all, > > Suppose I've created a Hits object by > all_hits <- findOverlaps(query, subject, select = 'all', type = 'any') > and now I want to get the first (or last) hit for each query. Of course, I could use > first_hits <- findOverlaps(query, subject, select = 'first', type = 'any') > last_hits <- findOverlaps(query, subject, select = 'last', type = 'any') > but I this isn't necessary as all the required information is in the all_hits Hits object. > > I was unable to find a function to do what I wanted, however, based at the source for findOverlaps-methods.R (actually Hector's branch at https://github.com/hcorrada/GenomicRanges/blob/master/R/findOverlaps- methods.R) I wrote the following simple functions > getFirstHit <- function(all_hits){ > ans <- rep.int(NA_integer_, queryLength(all_hits)) > oo <- IRanges:::orderIntegerPairs(queryHits(all_hits), subjectHits(all_hits), decreasing = TRUE) > ans[queryHits(all_hits)[oo]] <- subjectHits(all_hits)[oo] > return(ans) > } > getLastHit <- function(all_hits){ > ans <- rep.int(NA_integer_, queryLength(all_hits)) > ans[queryHits(all_hits)] <- subjectHits(all_hits) > return(ans) > } > > These do what I want and are faster than re-running findOverlaps for my use case (millions of query intervals with tens of thousands of subject intervals) > > Now to my questions: > (1) Did I just overlook built-in "getFirstHit" and "getLastHit" functions? > (2) Would others find "getFirstHit" and "getLastHit" useful enough to justify their inclusion in GenomicRanges (or IRanges, wherever it belongs)? > (3) I recall some discussion on this mailing list and Rdevel stating that using ":::" to access non-exported functions isn't a great idea for use in package code. If I need to include my own "getFirstHit" would someone be so kind as to point me to the best advice for avoiding calls to ":::" in my code to access IRanges:::orderIntegerPairs(queryHits)? > > Many thanks, > Pete > -------------------------------- > Peter Hickey, > PhD Student/Research Assistant, > Bioinformatics Division, > Walter and Eliza Hall Institute of Medical Research, > 1G Royal Parade, Parkville, Vic 3052, Australia. > Ph: +613 9345 2324 > > hickey at wehi.edu.au > http://www.wehi.edu.au > > > ______________________________________________________________________ > The information in this email is confidential and intend...{{dropped:8}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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@michael-lawrence-3846
Last seen 14 months ago
United States
Thanks for providing this use case. It's actually documented that the Hits are sorted by query. So using that assumption, an Rle-based approach like that provided by Harris is probably the most efficient. But I would use Rle from IRanges instead of the base "rle" class, because it offers more conveniences; for example, the code is pretty intuitive for this use case: queryHits_rle <- Rle(queryHits(all_hits)) first_hits <- all_hits[start(queryHits_rle)] last_hits <- all_hits[end(queryHits_rle)] Michael On Sun, Oct 20, 2013 at 1:32 PM, Peter Hickey <hickey@wehi.edu.au> wrote: > Hi all, > > Suppose I've created a Hits object by > all_hits <- findOverlaps(query, subject, select = 'all', type = 'any') > and now I want to get the first (or last) hit for each query. Of course, I > could use > first_hits <- findOverlaps(query, subject, select = 'first', type = 'any') > last_hits <- findOverlaps(query, subject, select = 'last', type = 'any') > but I this isn't necessary as all the required information is in the > all_hits Hits object. > > I was unable to find a function to do what I wanted, however, based at the > source for findOverlaps-methods.R (actually Hector's branch at > https://github.com/hcorrada/GenomicRanges/blob/master/R /findOverlaps-methods.R) > I wrote the following simple functions > getFirstHit <- function(all_hits){ > ans <- rep.int(NA_integer_, queryLength(all_hits)) > oo <- IRanges:::orderIntegerPairs(queryHits(all_hits), > subjectHits(all_hits), decreasing = TRUE) > ans[queryHits(all_hits)[oo]] <- subjectHits(all_hits)[oo] > return(ans) > } > getLastHit <- function(all_hits){ > ans <- rep.int(NA_integer_, queryLength(all_hits)) > ans[queryHits(all_hits)] <- subjectHits(all_hits) > return(ans) > } > > These do what I want and are faster than re-running findOverlaps for my > use case (millions of query intervals with tens of thousands of subject > intervals) > > Now to my questions: > (1) Did I just overlook built-in "getFirstHit" and "getLastHit" functions? > (2) Would others find "getFirstHit" and "getLastHit" useful enough to > justify their inclusion in GenomicRanges (or IRanges, wherever it belongs)? > (3) I recall some discussion on this mailing list and Rdevel stating that > using ":::" to access non-exported functions isn't a great idea for use in > package code. If I need to include my own "getFirstHit" would someone be so > kind as to point me to the best advice for avoiding calls to ":::" in my > code to access IRanges:::orderIntegerPairs(queryHits)? > > Many thanks, > Pete > -------------------------------- > Peter Hickey, > PhD Student/Research Assistant, > Bioinformatics Division, > Walter and Eliza Hall Institute of Medical Research, > 1G Royal Parade, Parkville, Vic 3052, Australia. > Ph: +613 9345 2324 > > hickey@wehi.edu.au > http://www.wehi.edu.au > > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:13}}
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Thanks to Harris, Chuck and Michael for their solutions. Much appreciated. Pete On 21/10/2013, at 3:25 PM, Michael Lawrence wrote: > Thanks for providing this use case. > > It's actually documented that the Hits are sorted by query. So using that assumption, an Rle-based approach like that provided by Harris is probably the most efficient. But I would use Rle from IRanges instead of the base "rle" class, because it offers more conveniences; for example, the code is pretty intuitive for this use case: > > queryHits_rle <- Rle(queryHits(all_hits)) > first_hits <- all_hits[start(queryHits_rle)] > last_hits <- all_hits[end(queryHits_rle)] > > Michael > > > > On Sun, Oct 20, 2013 at 1:32 PM, Peter Hickey <hickey@wehi.edu.au> wrote: > Hi all, > > Suppose I've created a Hits object by > all_hits <- findOverlaps(query, subject, select = 'all', type = 'any') > and now I want to get the first (or last) hit for each query. Of course, I could use > first_hits <- findOverlaps(query, subject, select = 'first', type = 'any') > last_hits <- findOverlaps(query, subject, select = 'last', type = 'any') > but I this isn't necessary as all the required information is in the all_hits Hits object. > > I was unable to find a function to do what I wanted, however, based at the source for findOverlaps-methods.R (actually Hector's branch at https://github.com/hcorrada/GenomicRanges/blob/master/R/findOverlaps- methods.R) I wrote the following simple functions > getFirstHit <- function(all_hits){ > ans <- rep.int(NA_integer_, queryLength(all_hits)) > oo <- IRanges:::orderIntegerPairs(queryHits(all_hits), subjectHits(all_hits), decreasing = TRUE) > ans[queryHits(all_hits)[oo]] <- subjectHits(all_hits)[oo] > return(ans) > } > getLastHit <- function(all_hits){ > ans <- rep.int(NA_integer_, queryLength(all_hits)) > ans[queryHits(all_hits)] <- subjectHits(all_hits) > return(ans) > } > > These do what I want and are faster than re-running findOverlaps for my use case (millions of query intervals with tens of thousands of subject intervals) > > Now to my questions: > (1) Did I just overlook built-in "getFirstHit" and "getLastHit" functions? > (2) Would others find "getFirstHit" and "getLastHit" useful enough to justify their inclusion in GenomicRanges (or IRanges, wherever it belongs)? > (3) I recall some discussion on this mailing list and Rdevel stating that using ":::" to access non-exported functions isn't a great idea for use in package code. If I need to include my own "getFirstHit" would someone be so kind as to point me to the best advice for avoiding calls to ":::" in my code to access IRanges:::orderIntegerPairs(queryHits)? > > Many thanks, > Pete > -------------------------------- > Peter Hickey, > PhD Student/Research Assistant, > Bioinformatics Division, > Walter and Eliza Hall Institute of Medical Research, > 1G Royal Parade, Parkville, Vic 3052, Australia. > Ph: +613 9345 2324 > > hickey@wehi.edu.au > http://www.wehi.edu.au > > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:31}}
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Charles Berry ▴ 290
@charles-berry-5754
Last seen 3.9 years ago
United States
Peter Hickey <hickey at="" ...=""> writes: > > Hi all, > > Suppose I've created a Hits object by > all_hits <- findOverlaps(query, subject, select = 'all', type = 'any') > and now I want to get the first (or last) hit for each query. Of course, > [...] gr1 <- GRanges(rep(letters,each=10), IRanges(start=sample(1e6,260),width=20)) hit1 <- findOverlaps( gr1, gr1, maxgap=1e5) hit1 # show what hit1 is hit1[!duplicated(queryHits(hit1))] # only the first hit for each query value hit1[!duplicated(queryHits(hit1),fromLast=TRUE)] # only last hits HTH, Chuck
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