Entering edit mode
7.0 years ago
whgsnp
•
0
Hi there,
I'm at a beginner level using R/Bioconductor. I'm currently trying to read in RNA-seq bed files from local and web (UCSC) sources and then hand over the score of every chromosome separately to a wavelet transform (packages "Wavelets", "WaveletComp"). Could you give me a brief instruction how to proceed? I would be very grateful for your help.
Cheers! SNP
1) I can't find "Wavelets" and "WaveletComp" in Bioconductor, are you sure those are the right names? (please provide links)
2) RTM (Read that manual), a very old zen proverb. In every Bioconductor package page there is a small table with the so called Vignettes and the PDF manual, 99% of the cases they come with examples and quick-start tutorials which are worth reading through. ;)
Thank you so much. "Wavelets" and "WaveletComp" are R packages: https://cran.r-project.org/web/packages/wavelets/index.html https://cran.r-project.org/web/packages/WaveletComp/index.html And you're right, the examples for analysis are there, I was just wondering what might be the quickest workflow for the combination of the two tasks: 1) Reading-in of bed files from different sources with splitting of individual chromosomes 2) Wavelet transforms of individual chromosomes
Would you recommend using GRanges for 1) ?
You should nest this comment as "reply" to your first question, as this room is only for answers to your original question and not for comments on it (telling you before the admins will tell you :D)
I haven't used those packages at all in my entire life, I can't tell you! I could only tell you about the manuals, because I used many other R packages and the manuals always proved trustworthy :)
OK, I got it. Thank you for your help.
I moved this to comment, see remark from Macspider.