User: Saroj Mohapatra

gravatar for Saroj Mohapatra
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Posts by Saroj Mohapatra

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Comment: C: building enzyme centric metabolic network
... Hi Martin: Thanks a lot. This _is_ a much better way of creating the incidence matrix. Saroj Martin Morgan wrote: > Hi Saroj -- > > All those 'for' loops and the idea that you'd have to 'monitor > progress' make me think there's a better way to do this. Without > commenting on the me ...
written 10.0 years ago by Saroj Mohapatra450
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Answer: A: building enzyme centric metabolic network
... Hi Anupam: Using your second criterion, i.e., two enzymes are linked if they are in the same pathway, one strategy would be to use the information from org. packages for creating a network for each species. # For mouse, use the package org.Mm.eg.db to get the list of all entrez ids, associated KEG ...
written 10.0 years ago by Saroj Mohapatra450
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Answer: A: Visualize KEGG pathway
... Hi Tim: It is possible to set the foreground and background colors for each node in the KEGG pathway through bg.color.list and fg.color.list arguments of the function color.pathway.by.objects. I color just one node below in white-on-blue, rest all in black-on-white. > library("KEGGSOAP") Loadin ...
written 10.0 years ago by Saroj Mohapatra450
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Answer: A: Retrieving KEGG pathway diagrams via KEGGSOAP
... Hi Daren, I do not know why but if you try with more than one node, the code works. > url <- mark.pathway.by.objects("path:hsa03050", c("hsa:5709", "hsa:10197")) > url [1] "http://soap.genome.jp/tmp/mark_pathway_www2_api15820/hsa03050.gif" > if(interactive()){ browseURL(url) } Best ...
written 10.0 years ago by Saroj Mohapatra450
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Answer: A: evaluating a character string as a variable name in an ExpressionSet object
... Hi Kavitha: Are you looking for something like this: > ls() character(0) > # I have a string called "reallyfunnyvariable" > mystr = "reallyfunnyvariable" # I want to convert this to a variable with the same name; I want it to be a list eval(parse(text=paste(mystr,"=list()",sep=""))) # N ...
written 10.0 years ago by Saroj Mohapatra450
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Comment: C: Visualise KEGG pathway and highlight genes
... Hi, I am sorry, the code from KEGGSOAP manual was incomplete in my last email. It actually reads: -------------- url <- mark.pathway.by.objects("path:eco00260", c("eco:b0002", "eco:c00263")) if(interactive()){ browseURL(url) } url <- color.pathway.by.objects("path:eco ...
written 10.0 years ago by Saroj Mohapatra450
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Answer: A: Visualise KEGG pathway and highlight genes
... Hi Daniel: This is also something in which I am interested, but have not found an easy way yet. If KEGG allows the network images to be downloaded in SVG format (currently I found only GIF), then I think there is a way of manually modifying the color of the nodes. Within the KEGGSOAP package, the ...
written 10.0 years ago by Saroj Mohapatra450
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Comment: C: question about heatmap.2
... Hi Wei, I think you need to set the row.names argument in read.csv to 1. > ?read.csv ----------------------- row.names: a vector of row names. This can be a vector giving the actual row names, or a single number giving the column of the table which contains the row names, o ...
written 10.1 years ago by Saroj Mohapatra450
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Answer: A: GOLOCUSID
... Hi John: I do not have a general answer. However, the "org." packages do have a mapping from GO to Entrez gene. For example, there is the mouse package org.Mm.eg.db that has org.Mm.egGO which maps between the two identifiers. > library("org.Mm.eg.db") > ?org.Mm.egGO2EG ----------- org.M ...
written 10.1 years ago by Saroj Mohapatra450
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Answer: A: heatmap output problems in pdf
... Hi Pete: It is difficult for others to know what the problem is unless you send some code that would reproduce the error. For example, the following three lines would create a pdf document (in the working directory) with the image of a plot. > pdf(file="temp.pdf") > plot(1:10) > dev.off() ...
written 10.1 years ago by Saroj Mohapatra450

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