Description Usage Arguments Value Author(s) See Also Examples
View source: R/BI_SequenceMotif.R
co-motif exploration for sequence
1 2 | SequenceMotif(sequence, motif, base = c("A", "C", "U", "G"),
verbose = T)
|
sequence |
a vector of sequences |
motif |
a charactor or numeric motif |
base |
the type of base.Default is |
verbose |
whether do reports |
a list contain counts and sequences information of motifs
Weibin Huang<654751191@qq.com>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | ## Create some random sequences
sequence <- NULL
for(i in 1:100){
set.seed(i);
j <- sample(18:21,1)
s.i <- sample(c("A","C","U","G"),j,replace = T)
s.i <- paste(s.i,collapse = "")
sequence <- c(sequence,s.i)
}
## explore two 4-base motifs
motif <- c("CCGU","GGAU")
l <- SequenceMotif(sequence,motif)
View(l$Counts)
View(l$Sequence)
l$Sequence$GGAU
## explore all 3-base or 4-base motifs
motif <- c(3,4)
l <- SequenceMotif(sequence,motif)
View(l$Counts)
View(l$Sequence)
l$Sequence$GGAU
|
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