Michael, Thanks, forgot about the row comma. That got it to work! session info was: > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomicRanges_1.12.5 IRanges_1.18.4 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] stats4_3.0.1 tools_3.0.1 On Tue, Nov 26, 2013 at 2:02 PM, Michael Lawrence <lawrence.michael@gene.com> wrote: > > > > On Tue, Nov 26, 2013 at 10:55 AM, Giovanni Carosso <gacarosso@gmail.com>wrote: > >> Hi Tim and Michael, >> >> Thanks so much for the responses. >> >> I tried Tim's method for subsetting my csv file for lines that overlap >> two other csv's, which was: >> >> require(GenomicRanges) >> tbl <- read.csv(file1) >> >> GR1 <- as(tbl, 'GRanges') >> GR2 <- as(read.csv(file2), 'GRanges') >> GR3 <- as(read.csv(file3), 'GRanges') >> >> lines_in_file1_over_2and3 <- queryHits(findOverlaps(GR1, >> intersect(GR2,GR3))) >> >> But, I got errors saying that data.frame(from read.csv) cannot be coerced >> into GRanges. I then tried a similar approach by first turning each file >> into GRanges, then using queryHits,findOverlaps. This generated an integer >> list, but I'm not sure how to then pull out these lines from the original >> csv file, to include all the columns in addition to the chrom, start, end. >> Should I change the files somehow before running Tim's code? >> >> Here's some dummy code I used: >> >> > GR1 <- as(tbl,'GRanges') >> Error in as(tbl, "GRanges") : >> no method or default for coercing “data.frame” to “GRanges” >> > > I'm guessing your GenomicRanges version is old, so the data.frame coercion > does not exist. Please attach your sessionInfo(). > > > class(tbl) >> [1] "data.frame" >> > GR1 <- GRanges(seqnames=tbl$chr, ranges=IRanges(start=tbl$start, >> end=tbl$end)) >> > GR2 <- GRanges(seqnames=tbl1$chr, ranges=IRanges(start=tbl1$start, >> end=tbl1$end))> GR3 <- GRanges(seqnames=tbl2$chr, >> ranges=IRanges(start=tbl2$start, end=tbl2$end)) >> > lines_in_1_over2and3 <- queryHits(findOverlaps(GR1, intersect(GR2,GR3))) >> > head(lines_in_1_over2and3) >> [1] 2 3 4 6 8 10 >> > test <- tbl[lines_in_1_over2and3] >> Error in `[.data.frame`(tbl, lines_in_1_over2and3) : >> undefined columns selected >> >> > Those are row indices, so you need: > test <- tbl[lines_in_1_over2and3,] > > >> >> Sorry if these are kind of naive questions, I'm new to this kind of >> stuff. The main thing is that I want to make sure to extract all the >> columns out of the csv, in addition to chrom, start, end (which is why I >> think making BED file wouldn't work). >> >> > You can tabix any tab-separated file with chrom, start, end. And then > import with > rtracklayer::import(TabixFile(file1), which = GRanges(...)) > > > >> I very much appreciate the help! >> >> Giovanni >> >> >> On Wed, Nov 20, 2013 at 1:26 AM, Tim Triche, Jr. <tim.triche@gmail.com>wrote: >> >>> Hi Michael, >>> >>> Is it the case that BED files can be comma-separated values e.g. >>> chrom,chromStart,chromEnd,otherStuffNotInBed9FileDefinition >>> ? >>> >>> Because, otherwise, it seems like >>> >>> require(GenomicRanges) >>> tbl <- read.csv(file1) >>> GR1 <- as(tbl, 'GRanges') >>> >>> GR2 <- as(read.csv(file2), 'GRanges') >>> GR3 <- as(read.csv(file3), 'GRanges') >>> >>> lines_in_file1_over_2and3 <- queryHits(findOverlaps(GR1, >>> >>> intersect(GR2,GR3))) >>> >>> might be the most straightforward way to get the requested line numbers. >>> (?) >>> >>> Now if he has actual BED files already, then obviously your method is >>> better, and I am making a note of this trick for later (I have been >>> TABIX'ing my BEDs & other tab-delimited genome-format files ever since you >>> added support for it). >>> >>> Thanks for the tip, >>> >>> --t >>> >>> >>> >>> *He that would live in peace and at ease, * >>> *Must not speak all he knows, nor judge all he sees.* >>> >>> Benjamin Franklin, Poor Richard's Almanack<http: archive.org="" details="" poorrichardsalma00franrich=""> >>> >>> >>> On Tue, Nov 19, 2013 at 5:21 PM, Michael Lawrence < >>> lawrence.michael@gene.com> wrote: >>> >>>> Simply run Rsamtools::bgzip() and indexTabix() on your BED file and then >>>> rtracklayer::import("my.bed.gz", which = roi_as_granges). >>>> >>>> >>>> >>>> >>>> On Tue, Nov 19, 2013 at 10:49 AM, Giovanni Carosso <gacarosso@gmail.com>>>> >wrote: >>>> >>>> > Hello, >>>> > >>>> > I have three CSV files of genomic intervals (chromosome start, stop, >>>> plus >>>> > other information in different columns) each containing between >>>> 10k-20k >>>> > lines. >>>> > >>>> > I am looking for a way to pull out from one file only the lines that >>>> have >>>> > genomic overlap with both of the other two files. In other words, >>>> subset >>>> > file A to include only the lines of file A whose interval overlaps >>>> > intervals in Files B and C. >>>> > >>>> > I'm able to create GRanges and manipulate these to get the subsetted >>>> > GRanges list, but I have not found a way to then use this GRanges as >>>> an >>>> > index to pull out the proper lines from CSV file. >>>> > >>>> > Is there a simple way to subset my file in this way that I'm missing? >>>> > >>>> > Thanks, >>>> > Giovanni >>>> > >>>> > [[alternative HTML version deleted]] >>>> > >>>> > _______________________________________________ >>>> > Bioconductor mailing list >>>> > Bioconductor@r-project.org >>>> > https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> > Search the archives: >>>> > http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> > >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> >> > [[alternative HTML version deleted]]