User: Fahim Md

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Fahim Md250
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Posts by Fahim Md

<prev • 25 results • page 1 of 3 • next >
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Comment: C: Genomic Ranges. Ignore strandedness in findOverlap function.
... Thanks Steve. I resolved the problem. Actually I was using ignore.strand option with RangedData object. Thanks again. Fahim On Fri, Jan 6, 2012 at 4:41 PM, Steve Lianoglou < mailinglist.honeypot@gmail.com> wrote: > Hi Fahim, > > > On Fri, Jan 6, 2012 at 4:08 PM, Fahim Mohammad ...
written 8.0 years ago by Fahim Md250
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Comment: C: Genomic Ranges. Ignore strandedness in findOverlap function.
... Hi Steve I can see that statement in the findOverlaps method. Do I need to write my own function to do this as 'ignore.strand' is not an allowed argument in standard function. What are the steps to do this? Thanks Fahim On Fri, Jan 6, 2012 at 4:41 PM, Steve Lianoglou < mailinglist.honeypot@gma ...
written 8.0 years ago by Fahim Md250
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Genomic Ranges. Ignore strandedness in findOverlap function.
... Hi findOverlap function depends on the 'strand'edness of the subject and query. In the example below, I am using findOverlap function to find overlapping ranges. Is there a way to completely ignore this feature and report all overlaps. grSubject <- GRanges( seqnames =Rle(rep("chr1", 7)), range ...
written 8.0 years ago by Fahim Md250 • updated 8.0 years ago by Steve Lianoglou12k
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Answer: A: GRanges - coercion from dataframe
... Brute force method to do the same. load('/home/fahim/rugit/rangeData/hg19/GeneName.RData') head(data) fldslen = length(names(data)) #how many fields gr = GRanges(seqnames = Rle(data$seqnames), IRanges(data$start, data$end), strand = Rle(as.character(data$strand)), name = data$name ) if (fldslen &g ...
written 8.1 years ago by Fahim Md250
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GRanges - coercion from dataframe
... Hi I generated a data frame from GRanges object by performing data = as.data.frame (grObj, row.names =NULL); #grObject is GRanges object having 'seqnames' as one of its field. save (data, file = ..) Now I want to read this data file again as GRanges object. Is there any built-in method to do th ...
convert iranges written 8.1 years ago by Fahim Md250
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Comment: C: GRanges - reduce() function
... Hi Herves Thanks a lot for your reply. I also feel that adding suffix in the output of unlist() function is not useful. Fahim 2011/11/18 Hervé Pagès > Hi Fahim and others, > > > On 11-11-18 07:45 AM, Fahim Mohammad wrote: > >> Thanks a lot Vincent, >> Your suggestion ...
written 8.2 years ago by Fahim Md250
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Comment: C: GRanges - reduce() function
... Thanks a lot Vincent, Your suggestion helped me a lot, but the problem of mangled names and unsorted ranges remained. Also the 'unlist' function add sufiix in the name. > unlist(reduce(split(gr, elementMetadata(gr)$Gene)))GRanges with 4 ranges and 0 elementMetadata values: seqnames ra ...
written 8.2 years ago by Fahim Md250
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GRanges - reduce() function
... Hi In the following example, I am trying to use 'reduce()' function to reduce the genomic intervals and find intervals corresponding to 'Gene'. It is behaving as it is desired. However the output of the reduce just give the intervals (I am losing the 'Gene' metadata). Is there a way to retain 'Gene ...
written 8.2 years ago by Fahim Md250 • updated 8.1 years ago by Jason Ross20
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Comment: C: Augmenting metadata values in GRanges object
... Thanks Peter, elementMetadata(gr)[["toAdd"]] = 1:10 worked for me. Cheers!!! Fahim On Tue, Nov 15, 2011 at 8:46 PM, Martin Morgan wrote: > On 11/15/2011 05:31 PM, Martin Morgan wrote: > >> On 11/15/2011 03:50 PM, Fahim Mohammad wrote: >> >>> Hi >>> Is the ...
written 8.2 years ago by Fahim Md250
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Augmenting metadata values in GRanges object
... Hi Is there a function to augment metadata into an already built GRanges object? For example (ex from vignette) > gr <- GRanges(seqnames = Rle(c("chr1", "chr2", "chr1",+ "chr3"), c(1, 3, 2, 4)), ranges = IRanges(1:10, end = 7:16,+ names = head(letters, 10)), strand = Rle(strand(c("-" ...
written 8.2 years ago by Fahim Md250 • updated 8.2 years ago by Martin Morgan ♦♦ 24k

Latest awards to Fahim Md

Popular Question 8.0 years ago, created a question with more than 1,000 views. For using Blat in R
Popular Question 8.0 years ago, created a question with more than 1,000 views. For GRanges - reduce() function
Popular Question 8.0 years ago, created a question with more than 1,000 views. For GRanges - coercion from dataframe

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