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quick start section added

paul-shannon authored on 09/04/2020 15:37:49
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@@ -41,3 +41,28 @@ Still, motif-matching to DNA sequence plays an important role in identifying gen
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 # Quick Start
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+CTCF is a DNA-binding factor regulating the 3D structure of
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+chromatin^[CTCF: Master Weaver of the Genome, Philips and Corces, 2009, Cell.  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3040116].
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+What is its binding motif?  
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+
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+The MotifDb **query** function performs a broad, case-neutral text search through all the metadata (all the annotation) for all of
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+the motifs.  It returns a list of matching motifs.  More information about the metadata is provided below.
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+
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+We begin with a simple search, retrieving all motifs annotated with the case-neutral string "CTCF".
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+
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+```{r load MotifDb, query CTCF, prompt=FALSE, message=FALSE, results="show"}
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+library(MotifDb)
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+query(MotifDb, "CTCF")
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+```
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+
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+Let us sharpen the search, looking only for human Jaspar 2018, or HOCOMOCO v11 core motifs, category "A". Eliminate "CTCFL".
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+
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+```{r query CTCF human, prompt=FALSE, message=FALSE, results="show"}
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+library(MotifDb)
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+query(MotifDb, andStrings=c("CTCF", "hsapiens"),
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+               orStrings=c("jaspar2018", "hocomocov11-core-A"),
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+               notStrings="ctcfl")
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+```
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+
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+
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+# References