search for: findoverlaps

Hi How to access the values in the output that is an object of S4 type. I tried to access using subset ( [ ] ) but it is not allowed. Any clue?? Thanks -- Fahim #My code is as follows: require(IRanges); query <- IRanges(c(1, 4, 9), c(5, 7, 10)) subject <- IRanges(c(2, 2, 10), c(2, 3, 12)) findOverlaps(query, subject) Output of find overlap function is: ------------------ 1> findOverlaps(query, tree) An object of class "RangesMatching" Slot "matchMatrix": query subject [1,] 1 1 [2,] 1 2 [3,] 3 2 Slot "DIM": [1] 4 3 -----------...

...) { ##### MATCH THE POSITIVE STRAND ###### #need to get start and end positions (end = start + (length-1)) gr <- GRanges( seqnames = rep(i,nrow(mp)), ranges = IRanges(start = mp[[1]], end = mp[[1]]+(mp[,2]-1)), strand = rep("+", nrow(mp))) #OL <- findOverlaps(query=gr, subject=annotGr) OL.p <- annotGr[(!is.na(match(annotGr, gr)))] #as.data.frame(OL) ## view the results #tdata.p <- annotGr[unique(queryHits(OL)),] #tdata.p <- as.data.frame(tdata.p, row.names = NULL, optional = FALSE) #write.table(tdata.p, paste(i,"plus....

Hi: I have a two large files (over 300K lines). file 1: Name X UK 199 UK 230 UK 139 ...... UAE 194 UAE 94 File 2: Name X Y UK 140 180 UK 195 240 UK 304 340 .... I want to select X of File 1 and search if it falls in range of X and Y of File 2 and Print only those lines of File 1 that are in range of File 2 X and Y How can it be done it

Hi everybody, I would like to know whether it is possible to compare to tables for certain parameters. I have these two tables: gene table name chr start end str accession Length gen1 4 646752 646838 + MI0005806 86 gen12 2L 243035 243141 - MI0005821 106 gen3 2L 159838 159928 + MI0005813 90 gen7 2L

Hi, I want to merge multiple chromosomal regions based on their common intersecting regions. I tried couple of things using while and if loops but did not work out. I would appreciate if anyone could provide me a small piece of code in R to get the intersection of following example: chr1: 100-150 chr1: 79-250 chr1: 100-175 chr1: 300-350 I want the intersection of all four regions as follow:

Hi All, I have an CBS segmentation algorithm output for 10 tumor samples each from 2 different tumors. Now, I am in an urgent need to assign gene (followed by all genes present) that belong to a particular segment after I removed all the CNVs from segment data. The format of the data is: Sample Chromosome Start End Num_Probes Segment_Mean Sample1A-TA 1 51598 76187 15

Hello, I'm trying to use coxph() function to fit a very simple Cox proportional hazards regression model (only one covariate) but the parameter space is restricted to an open set (0, 1). Can I still obtain a valid estimate by using coxph function in this scenario? If yes, how? Any suggestion would be greatly appreciated. Thanks!!! [[alternative HTML version deleted]]