Question: Bioconductor RNA-seq bed file read-in/download then wavelet transform
0
gravatar for whgsnp
2.4 years ago by
whgsnp0
Rome
whgsnp0 wrote:

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

rna-seq bed files wavelet • 525 views
ADD COMMENTlink modified 2.3 years ago by shepherl ♦♦ 1.4k • written 2.4 years ago by whgsnp0
Answer: Bioconductor RNA-seq bed file read-in/download then wavelet transform
0
gravatar for shepherl
2.3 years ago by
shepherl ♦♦ 1.4k
United States
shepherl ♦♦ 1.4k wrote:

The Bioconductor package rtracklayer provides for reading in bed files.

 

source("https://bioconductor.org/biocLite.R")

biocLite("rtracklayer")

library("rtracklayer")

?BEDFile

 

I'm not exactly sure what you mean by score of every chromosome, is that something that is provided in the file or is it something that requires calculation? 

ADD COMMENTlink written 2.3 years ago by shepherl ♦♦ 1.4k
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