Lolliplot graph for mutations

Question

[kavikrish1996]

Hi everyone,

I'm new to using bioinformatics and specifically I would like to create a lolliplot graph for some mutations I have for a bacterium. However I've been struggling IMMENSELY using bioconductor packages or R studio in general and in actual fact I have no idea what I am doing? How do I go about doing this?

I used this code from "trackViewer Vignette" (https://www.bioconductor.org/packages/release/bioc/vignettes/trackViewer/inst/doc/trackViewer.html#lolliplot) for which I downloaded this package from Bioconductor using R, opened the trackviewer file on R studio but as I have no experience at all I'm not sure how to go about creating this graph?

Thank you in advance,

Kavi

[h.mon]

If you have been struggling, it means you tried some code and had some error messages. Edit your post to include the code you tried, and the errors you got. Ideally, you should include some small dataset so we can easily replicate your efforts.

[kavikrish1996]

Thank you for your reply.

Yes sorry about that, I used this code from "trackViewer Vignette" (https://www.bioconductor.org/packages/release/bioc/vignettes/trackViewer/inst/doc/trackViewer.html#lolliplot) for which I downloaded this package from Bioconductor using R, opened the trackviewer file on R studio but as I have no experience at all I'm not sure how to go about creating this graph?

Answer 1

[H.Hasani]

in the site you mentioned there are number of things you need to understand correctly:

• snp: this variable contatins contains the basic info of each mutation's position, e.g. in gene XXX on chr1:12345
• sample.gr: create a genomic interval object out of you list of mutations
• features: the genomic intervals; i.e. you create intervals of the genes in your list (including XXX) in which the correct genomic positions of each gene is given

note that the mutation's positions should be within the features, e.g. one interval in the variable features should start at position <= 12345 and ends at >=12345

to obtain the genomic positions of the gene you need a reference file (gencode, ucsc, etc.)

hth