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...chPattern(query.minus, Hsapiens[[i]], fixed=FALSE, max.mismatch=5) mm <- as.matrix(matches.minus.strand) OL.p <- NULL if(nrow(mp) > 0) { ##### 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 &l...

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]]

I do have a bunch of genes ( nearly ~50000) from the whole genome, which read in genomic ranges A range(gene) can be seem as an observation has three columns chromosome, start and end, like that seqnames start end width strand gene1 chr1 1 5 5 + gene2 chr1 10 15 6 + gene3 chr1 12 17 6 + gene4 chr1 20 25 6 + gene5 chr1 30 40 11 + I just wondering is there an efficient way to find overlapped, upstream and dow...

I've got two tables.... first one(table1): ID chrom start end Ex1 2 152 180 Ex2 10 2000 2220 Ex3 15 3000 4000 second one ( table2): chrom location name 2 160 Alv 2 190 GNN 2 100

...mous>: no visible global function definition for ?endoapply?\n <anonymous>: no visible binding for global variable ?reduce?\n <anonymous> : <anonymous>: no visible global function definition for ?alignPairs2Tx?\n <anonymous>: no visible global function definition for ?seqnames?\n <anonymous> : <anonymous> : <anonymous>: no visible global function definition for ?alignPairs2Tx?\n <anonymous> : <anonymous>: no visible global function definition for ?alignPairs2Ex?\n <anonymous>: no visible global function definition for ?seqnames?\n...

I do have a bunch of genes ( nearly ~50000) from the whole genome, which read in genomic ranges A range(gene) can be seem as an observation has three columns chromosome, start and end, like that seqnames start end width strand gene1 chr1 1 5 5 + gene2 chr1 10 15 6 + gene3 chr1 12 17 6 + gene4 chr1 20 25 6 + gene5 chr1 30 40 11 + I just wondering is there an efficient way to find *overlapped, upstream and do...

Hello, I have start and end coordinates from different experiments (DNase hypersensitivity data) and now I would like to combine overlapping intervals. For instance (see my test data below) (2) 30-52 and (3) 49-101 are combined to 30-101. But 49-101 and 70-103 would not be combined because they are on different chromosomes (chr a and chr b). Does anybody have an idea? Thanks Hermann > df

I have just placed version 0.2 alpha of my library, dna, on my web page at www.luc.ac.be/~jlindsey/rcode.html The R functions in this library cover most of the basic methods of dna and protein sequence analysis. The library includes ports of CLUSTAL W for multiple sequence alignment and flip for finding open reading frames in a dna sequence. There are an enormous number of interesting and

I have just placed version 0.2 alpha of my library, dna, on my web page at www.luc.ac.be/~jlindsey/rcode.html The R functions in this library cover most of the basic methods of dna and protein sequence analysis. The library includes ports of CLUSTAL W for multiple sequence alignment and flip for finding open reading frames in a dna sequence. There are an enormous number of interesting and

...mous>: no visible global function definition for ?endoapply?\n <anonymous>: no visible binding for global variable ?reduce?\n <anonymous> : <anonymous>: no visible global function definition for ?alignPairs2Tx?\n <anonymous>: no visible global function definition for ?seqnames?\n <anonymous> : <anonymous> : <anonymous>: no visible global function definition for ?alignPairs2Tx?\n <anonymous> : <anonymous>: no visible global function definition for ?alignPairs2Ex?\n <anonymous>: no visible global function definition for ?seqnames?\n...