Thanks, I has worked out.
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#String operation#protein-protein interaction #R platform
I want to create an excel file where there are three columns
proteinA pp protein B
I have acquired the word file as follow from biogrid:
"ETG18033 ETG19698 Nfkb1 Relb NF-KB1|NF-kappaB|NF-kappaB1|p105|p50|p50/p105 shep Two-hybrid Ravasi T (2010) 20211142 10090 10090"
I want to process the file such that only proteins names are taken.
I am not so familiar on working with string. I wanted only protein which are Nfkb1 RelB i.e. the first two protein. How could I proceed with R platform?
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Ram
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slg.manti •
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slg.manti •
1 answer
Do not use Word or Excel - create a tab separated file and view it with a plain text editor. Excel can wreak havoc on gene names, and Word adds unnecessary metadata to plain text content.
You should really read up on R tutorials for string processing, especially functions like strsplit, paste and gsub. I am choosing to not provide exact code as it will help your learning process to use these pointers get to your end goal yourself.
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Please do not use
#in the title (as hashtags) - it makes no sense and adds no value. Also, please use the formatting bar (especially thecodeoption) to present your post better. You can use backticks for inline code (`text` becomestext), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.Looks like tab separated file,
myData <- read.table("myfile.txt")should work fine, then subset relevant column. Avoid Word/Excel, use plain text editors like Notepad++.Thanks, it is working