WGBS Data Analysis Related

Question

[shrinka.genetics]

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

1. in which format (file format) it has to be given?

   and

2. what is the command to make this extdata?

Thanks
Shrinka

[cpad0112]

1. Lister2009_imr90_hg18_chr22.tab (tab separated text file)
2. Navigate to the Lister2009_imr90_hg18_chr22.tab location (folder), open the file and see the content and format. Format your data according to it.

[shrinka.genetics]

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

[cpad0112]

from the manual:

In a first step, the Bis-seq data needs to be loaded into R. The data should be in a tab-delimited
file with four columns, chromosome, position, T and M, where position is the coordinate of the
cytosine in the CpG on the plus strand (we assume that the counts have been pooled from the
two strands), T is the total number of reads overlapping the cytosine and M the total number of
reads without cytosine to thymine conversion (reflecting methylated cytosines).

[shrinka.genetics]

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?

[cpad0112]

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.

1. 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.

2. extdata is the directory name where Lister2009_imr90_hg18_chr22.tab file is located.