User: Tim Smith

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Tim Smith1.1k
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Posts by Tim Smith

<prev • 102 results • page 2 of 11 • next >
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Comment: C: Graph of methylation data around TSS - Repitools or other package?
... Hi Dario, Thanks for those corrections. I now have the graph made. However, I'd like to modify the main title for the plot, the axis labels and the legend. I tried using xlab,ylab etc. to set the labels for the axes but get an error. Is there a way that I can do this? Pankaj On Saturday, Novemb ...
written 5.6 years ago by Tim Smith1.1k
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Comment: C: Graph of methylation data around TSS - Repitools or other package?
... Hi Dario, Thanks for the reply and the guidance. I think I'm almost there! So, here is my sample data. I make the featureScores object as you suggested, but get an error when I use it with binPlot: ################# ## test data ## CpG probe info probes <- data.frame(position=seq(1000, 3000, ...
written 5.6 years ago by Tim Smith1.1k
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Graph of methylation data around TSS - Repitools or other package?
... Hi, I have a small RRBS methylation dataset comprising of about 10000 CpG positions (rows) and 10 subjects (columns). I would like make a graph that shows the mean methylation of the CpG around the TSS, i.e. mean methylation on the Y-axis, and distance from TSS on the X-axis. I also have a file, do ...
go repitools written 5.6 years ago by Tim Smith1.1k • updated 5.6 years ago by Dario Strbenac1.4k
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Error: IdeogramTrack (Gviz)
... Hi, I believe I have the latest version of Gviz, but still get an error: > ideoTrack <- IdeogramTrack(genome="hg19", chromosome=3) Error in validObject(.Object) :   invalid class “Seqinfo” object: 'seqnames(x)' cannot contain zero-length or duplicated names Am I doing something wrong? ...
gviz written 6.0 years ago by Tim Smith1.1k • updated 6.0 years ago by Steve Lianoglou12k
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biomaRt: refseq gene details
... Hi, I was trying to get the gene details of refseq ids (these are output from blastn) with the following code: =================   library(biomaRt)   mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl")   attr <- c("refseq_mrna",'hgnc_symbol', 'chromosome_name','start_position','end_ ...
written 6.1 years ago by Tim Smith1.1k • updated 6.1 years ago by Steffen Durinck540
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Expected value of finding a sequence
... Hi, I was looking to find a package/function that would calculate the expected value/frequency of finding a subsequence, within a sequence of length L. For example, assuming that all nucleotides are equally probable, how many times would we expect to find the pattern 'ATTG' in a sequence of length ...
biostrings iranges written 6.3 years ago by Tim Smith1.1k
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biomaRt query: retrieve exon locations etc
... Hi All, Sorry for the naive question! I was trying to retrieve some coordinates (start and end positions) from biomaRt and I'm not sure if I'm doing things right… Problem definition: For a gene, retrieve the 5'UTR and exon coordinates for the most common isoform of the gene. *************** lib ...
biomart written 6.4 years ago by Tim Smith1.1k • updated 6.4 years ago by Steffen Durinck540
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Comment: C: BLAST - annotate package?
... Hi Jim, Thanks for the reply. I can get it to work even with the 2 without the quotes. But how do I get the values that I want (E-value, mismatches etc.) from the object returned by blastSequences? many thanks! ________________________________ From: James W. MacDonald Cc: bioc Sent: Friday, ...
written 6.8 years ago by Tim Smith1.1k
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BLAST - annotate package?
... Hi, Sorry for this basic question - I'm new to BLAST! I am trying to do BLAST (dna-nucleotide) for a sequence. I want to a sequence with the rhesus organism. I would like to get the following values: 1. Score (bits) 2. E-value 3. # Matches I am trying to use the 'annotate' package with the foll ...
organism written 6.8 years ago by Tim Smith1.1k • updated 6.8 years ago by James W. MacDonald50k
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Gviz : UcscTrack ..
... Hi, I was trying the code in the reference manual to get the GC content but it's giving errors. All the parameters appear to be correct (I checked with UCSC) - here is the code, as given in the manual: ############### from <- 65921878 to <- 65980988 gcContent <- UcscTrack(genome = "mm9", ...
go hgu133a written 6.9 years ago by Tim Smith1.1k

Latest awards to Tim Smith

Popular Question 5.1 years ago, created a question with more than 1,000 views. For installing 'lme4' package fails
Popular Question 5.1 years ago, created a question with more than 1,000 views. For org.Hs.eg.db -- Entrez ID to Gene Symbol conversion
Popular Question 5.1 years ago, created a question with more than 1,000 views. For Mapping gene symbols to gene names (org.Hs.eg.db?)
Popular Question 5.1 years ago, created a question with more than 1,000 views. For org.Hs.eg.db -- Entrez ID to Gene Symbol conversion
Popular Question 5.1 years ago, created a question with more than 1,000 views. For biomaRt: retrieve exon sequence, start and end positions
Centurion 5.1 years ago, created 100 posts.

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