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4.3 years ago
shrinka.genetics
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40
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 my input file. My question is
in which format (file format) it has to be given?
and
what is the command to make this extdata?
Thanks
Shrinka
tab
(tab separated text file)Lister2009_imr90_hg18_chr22.tab
location (folder), open the file and see the content and format. Format your data according to it.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 1 1 chr22 21971316 3 3
from the manual:
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?
Please refer to methylseekr manual. Your queries are addressed in the manual (https://www.bioconductor.org/packages/release/bioc/html/MethylSeekR.html). Copy/pasted from the manual.
One step of the MethylSeekR workflow depends on random permutations of the data (see below), which may lead to slightly different results each time the calculations are performed. It is thus recommended to set the random number generator seed at the beginning of the analysis to ensure exact reproducibility of the results.
extdata
is the directory name whereLister2009_imr90_hg18_chr22.tab
file is located.