October 2019
Intermediate to advanced
316 pages
9h 45m
English
Content preview from R Bioinformatics Cookbook
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How it works...
This is really neat code! In just a few lines, we were able to complete a whole analysis. We began by loading in a matrix description of a motif and some sequences we hope to find the promoter in—this happened in steps 1 and 2 and we got a universalmotif object and a DNAStringSet object to work with. The real work happens next, in steps 3 and 4. The scan_sequences() function searches each of the sequences and reports where it finds motifs—check out the motif_hits object to see where they are.
This will result in the following output:
## motif sequence start stop score max.score score.pct ## 1 YTTTYTTTTTYTTTY AT4G28150 73 87 7.531 22.45824 33.53335 ## 2 YTTTYTTTTTYTTTY AT4G28150 75 89 10.949 22.45824 48.75270
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