User: shrinka.genetics
shrinka.genetics • 0
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... Hello
I am working with WGBS Data. I am using MethyKit package.
MethyKit has provided a reference bed file in the extdata folder, which looks like below. My question is how can I find its header?
chr20 33506636 33563217 NM_007186 0 + 33513606 33562869 0 35 350,71,123,289,57,83,166,107 ...
written 7 months ago by
shrinka.genetics • 0
• updated
7 months ago by
cpad0112 ♦ 14k
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... I am using MethylKit package for WGBS Data analysis. With this package two annotation reference files are given refseq.hg18.bed and cpgi.hg18.bed. These are not complete file. From where I can get the whole file, so that I will be able to do the complete analysis with them. ...
written 7 months ago by
shrinka.genetics • 0
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7 months ago by
Kevin Blighe ♦ 69k
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Comment:
C: WGBS Data Analysis Related
... I have posted many questions, which one you are talking about?
Thanks
Shrinka ...
written 8 months ago by
shrinka.genetics • 0
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... Hello
I am working on WGBS Data. I am using MethylSeekR package
> library(MethylSeekR)
> set.seed(123)
> system.file("extdata", "Lister2009_imr90_hg18_chr22.tab",package="MethylSeekR")
I understand, my input file will go in the place of "Lister2009_imr90_hg18_chr22.tab". ...
written 8 months ago by
shrinka.genetics • 0
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Comment:
C: WGBS Data Analysis Related
... OK. Thanks. Now my question is
1) What is set.seed(123) ?
2) If I put my seq data in place of "Lister2009_imr90_hg18_chr22.tab" ,
then what is *extdata *then? ...
written 8 months ago by
shrinka.genetics • 0
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Comment:
C: WGBS Data Analysis Related
... Thanks
Lister2009_imr90_hg18_chr22.tab , contains these 4 columns
1) How can I get the header?
2) How can I get information about other chromosome?
chr22 21971222 20 19
chr22 21971252 8 8
chr22 21971269 3 3
chr22 21971308 ...
written 8 months ago by
shrinka.genetics • 0
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... Hello
I am working on WGBS Data. I am using MethylSeekR package. From vignette I can see that I can give my input file using the below mentioned command.
system.file("extdata", "Lister2009_imr90_hg18_chr22.tab",package="MethylSeekR")
As per my understanding is concerned, this extdata will be ...
written 8 months ago by
shrinka.genetics • 0
• updated
7 months ago by
Biostar ♦♦ 20
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... Could you please let me know that what is the input file format for Bioconductor package "Annotation"?
https://bioconductor.org/packages/release/workflows/html/annotation.html ...
written 8 months ago by
shrinka.genetics • 0
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Comment:
C: WGBS Data Analysis Related
... Yes it worked
Thanks
Shrinka ...
written 8 months ago by
shrinka.genetics • 0
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309
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Comment:
C: WGBS Data Analysis Related
... Thanks, I will work on that and will keep posting here.
What do you mean by text matrix?
Regards
Shrinka ...
written 8 months ago by
shrinka.genetics • 0
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