Description Usage Arguments Value Author(s) Examples
Perform enrichment analysis for (TF) motif footprinting
1 2 3 4 5 6 7 8 9 | ## S4 method for signature 'DsATAC'
getMotifFootprints(
.object,
motifNames,
samples = getSamples(.object),
motifFlank = 250L,
type = ".genome",
motifDb = "jaspar"
)
|
.object |
|
motifNames |
character vector of motif names |
samples |
sample identifiers |
motifFlank |
number of base pairs flanking the motif on each side |
type |
(PLACEHOLDER ARGUMENT: NOT IMPLEMENTED YET) character string specifying the region type or |
motifDb |
either a character string (currently only "jaspar" and sets contained in |
a list
of footprinting results with one element for each motif. Each motif's results contain summary data frames with aggregated counts
across all motif occurrences and a ggplot
object for plotting footprints
Fabian Mueller
1 2 3 4 5 6 7 8 9 | ## Not run:
dsa <- ChrAccRex::loadExample("dsAtac_ia_example")
motifNames <- c("MA1419.1_IRF4", "MA0139.1_CTCF", "MA0037.3_GATA3")
# motifNames <- grep("(IRF4|CTCF|GATA3)$", names(prepareMotifmatchr("hg38", "jaspar")$motifs), value=TRUE, ignore.case=TRUE) # alternative by searching
samples <- c("TeffNaive_U_1001", "TeffNaive_U_1002", "TeffMem_U_1001", "TeffMem_U_1002")
fps <- getMotifFootprints(dsa, motifNames, samples)
fps[["MA1419.1_IRF4"]]$plot
## End(Not run)
|
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