User: shrinka.genetics

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Posts by shrinka.genetics

<prev • 54 results • page 2 of 6 • next >
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Annotation Related after WGBS Data Analysis
... 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 ...
next-gen sequencing written 7 months ago by shrinka.genetics0 • updated 7 months ago by cpad011214k
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Reference file Annotation
... 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. ...
next-gen sequencing written 7 months ago by shrinka.genetics0 • updated 7 months ago by Kevin Blighe69k
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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.genetics0
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(Closed) WGBS Data Analysis Related
... 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". ...
next-gen sequencing written 8 months ago by shrinka.genetics0
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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.genetics0
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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.genetics0
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WGBS Data Analysis Related
... 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 ...
next-gen sequencing written 8 months ago by shrinka.genetics0 • updated 7 months ago by Biostar ♦♦ 20
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Annotation Related after WGBS Data Analysis
... 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 ...
gene written 8 months ago by shrinka.genetics0
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Comment: C: WGBS Data Analysis Related
... Yes it worked Thanks Shrinka ...
written 8 months ago by shrinka.genetics0
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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.genetics0

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