| TOP.Motif.ecdf {ORFik} | R Documentation |
Given sequences, DNA or RNA. And some score, scanning efficiency (SE), ribo-seq fpkm, TE etc.
TOP.Motif.ecdf(
seqs,
rate,
start = 1,
stop = max(nchar(seqs)),
xlim = c("q10", "q99"),
type = "Scanning efficiency"
)
seqs |
the sequences (character vector, DNAStringSet). See example below for input. |
rate |
a scoring vector (equal size to seqs) |
start |
position in seqs to start at (first is 1), default 1. |
stop |
position in seqs to stop at (first is 1), default max(nchar(seqs)), that is the longest sequence length |
xlim |
What interval of rate values you want to show type: numeric or quantile of length 2, 1. default c("q10","q99"). bigger than 10 percentile and less than 99 percentile. 2. Set to numeric values, like c(5, 1000), 3. Set to NULL if you want all values. Backend uses coord_cartesian. |
type |
What type is the rate scoring ? default ("Scanning efficiency") |
Top motif defined as a TSS of C and 4 T's or C's (pyrimidins) downstream of TSS C.
a ggplot gtable of the TOP motifs in 2 plots
## Not run:
if (requireNamespace("BSgenome.Hsapiens.UCSC.hg19")) {
txdbFile <- system.file("extdata", "hg19_knownGene_sample.sqlite",
package = "GenomicFeatures")
#Extract sequences of Coding sequences.
leaders <- loadRegion(txdbFile, "leaders")
# Should update by CAGE if not already done
cageData <- system.file("extdata", "cage-seq-heart.bed.bgz",
package = "ORFik")
leadersCage <- reassignTSSbyCage(leaders, cageData)
# Get region to check
seqs <- startRegionString(leadersCage, NULL,
BSgenome.Hsapiens.UCSC.hg19::Hsapiens, 0, 4)
# Some toy ribo-seq fpkm scores on cds
fpkm <- sample(1:115, length(leadersCage), replace = TRUE)
# Standard arguments
TOP.Motif.ecdf(seqs, fpkm, type = "ribo-seq FPKM")
# with no zoom on x-axis:
TOP.Motif.ecdf(seqs, fpkm, xlim = NULL)
}
## End(Not run)