Methylation profile through chromosome

Question

[Adam]

Hello,

I'm looking for some R package or even software to make methylation profile of chromosomes. I found two very nice packages for R:

ChromHeatMap (plots made by this are what I'm looking for) quantsmooth

Unfortunetaly my data isn't ExpressionSet or any object like this, so I don't know how to put it in. My data presentation(simple table in Excel with procentage methylation values):

TargetID    SYMBOL  CHR Position    cell_line_1 cell_line_2 cell_line_3
tag1    BRCA1   1   20771708    0,541441    0,4672899   0,3527385
tag2    BRCA1   1   20770604    0,3824306   0,59445525  0,408887625
tag3    GADPH   2   48719844    0,04331239  0,07833141  0,060533235
tag4    RASA1   3   100590962   0,0758754   0,12259825  0,11587337
tag5    RASA1   3   100589629   0,03625321  0,06974737  0,06018182
tag6    RASA1   3   100572000   0,05042755  0,090109245 0,10497023
tag7    ENG     5   98420934    0,3212603   0,16265565  0,137117475
tag8    ENG     5   98422056    0,1903218   0,19699885  0,491916625
tag9    CD5     4   114018313   0,1364216   0,127996    0,064798523
tag10   CD5     4   114018975   0,0766691   0,094443825 0,093477908

[WouterDeCoster]

Do you have an example how your plot should look like?

[Adam]

https://www.bioconductor.org/packages/devel/bioc/vignettes/ChromHeatMap/inst/doc/ChromHeatMap.pdf

[WouterDeCoster]

Please use ADD COMMENT/ADD REPLY to answer to other posts, as such we keep threads logically structured and easy to follow.

Answer 1

[Antonio R. Franco]

You can find information about how to get ExpressionSet data from this vignette