User: g.k

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Posts by g.k

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Comment: C: Selecting columns form a list of grange objects
... It is giving me incorrect number of dimensions  ...
written 18 days ago by g.k • 0
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Selecting columns form a list of grange objects
... I have a list having granges as follows:     $     File1.bed               GRanges object with 3 ranges and 2 metadata columns:                seqnames    ranges strand |        name                   <Rle> <IRanges>  <Rle> | <character>            [1]    chr1   [ 4,  6]    ...
granges R grange written 20 days ago by g.k • 0
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Concatenate a list of genomic ranges
... Hello, I have a list having granges as follows: $File1.bed GRanges object with 3 ranges and 2 metadata columns: seqnames ranges strand | name score <Rle> <IRanges> <Rle> | <character> <numeric> [1] chr1 [ 4, 6] + | ...
genomicranges granges R written 28 days ago by g.k • 0 • updated 28 days ago by James W. MacDonald ♦ 48k
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Detect Sites with Minimum Gap in GRanges Object
... Hello, I have a GRange object and I am using the findOverlaps() function inorder to control the minOverlap and maxGap. However I was wondering if there is a way to get the opposite? Is there a way to get the sites that have a  maxOverlap and the minGap?  seqnames     ranges        strand   chr1   ...
genomicranges granges R grange written 6 months ago by g.k • 0
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Comment: C: Detecting Overlaps within Grange Object
... Yes I do consider them overlapping  if they overlap by 1  position. Thank you I used findOverlaps() and it worked perfectly ! ...
written 6 months ago by g.k • 0
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Detecting Overlaps within Grange Object
... Hello, I have a Grange object which contains coordinates. I want to be able to remove the overlapping coordinates within the object following this rule : End(B) > Start(A) & End(A) > Start(B) so  I  remove Coordinate B For example : Chrom Start End Name Score Strand ...
iranges granges R grange written 6 months ago by g.k • 0 • updated 6 months ago by Michael Lawrence ♦ 10k
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Comment: C: How to know which Microarray Technique was used to processes the files
... Thank You ! ...
written 15 months ago by g.k • 0
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How to know which Microarray Technique was used to processes the files
... Hello, I have problem with analyzing microarray data sets. I have the GSM files and the GPL used which is GPL570, but how can I know if it is a 1 or 2 colored microarray technique used? ...
microarray R affymetrix microarrays written 15 months ago by g.k • 0 • updated 15 months ago by Axel Klenk • 920
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MA plot in R
... hello, I want to draw an MA plot  using plotWithHighlights() in R, however there are 2 simple arguments needed for this function which I'm not understanding how to use: status, and values. If someone can help me with them and probably give an example it would be great. Thank you very much ...
R rstudio plotma written 16 months ago by g.k • 0

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Popular Question 15 months ago, created a question with more than 1,000 views. For MA plot in R
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