lEnd and rStart positions act as
(1-based) coordinates of the innermost exonic nucleotides. They reside on
exon-intron boundaries and have one exonic and one intronic adjacent
nucleotide. The function counts width k-mers upstream on exonic
DNA in reading direction (left -> right on (+) strand, right -> left on
(-) strand).
countSpliceKmers(dna, seqid, lEnd, rStart, width, strand, k)character. Vector of DNA sequences. dna must
not contain other characters than "ATCGN".
Capitalization does not matter.
When a 'N' character is found, the current DNA k-mer is skipped.numeric. Vector of (1-based) values coding for one
of the given sequences.numeric. Vector of (1-based) left-end positions.
Will be used as rightmost window position.numeric. Vector of (1-based) right-start positions.
Will be used as leftmost window positions (over which(n-1) positions
overhang will be counted as part of frame).numeric. Vector of window width values.factor or numeric. First factor level (or numeric: 1)
value will be interpreted as (+) strand
For any other values, the reversed complement sequence will be
counted (in left direction from start value).
For (+) strand, the lEnd value will be used as starting position.
For (-) strand, the rStart position will be used as starting
positions.numeric. Number of nucleotides in tabled DNA motifs.
Only a single value is allowed (length(n) = 1 !)seq <- "acgtGTccccAGcccc"
countSpliceKmers(seq, seqid=1, lEnd=4, rStart=10, width=2, strand=1, k=3)
#
sq1 <- "TTTTTCCCCGGGGAAAA"
sq2 <- "TTTTTTTCCCCGGGGAAAA"
sq <- c(sq1, sq2)
seqid <- c( 1, 1, 2, 2)
lEnd <- c( 9, 9, 11, 11)
rStart <- c(14, 14, 16, 16)
width <- c( 4, 4, 4, 4)
strand <- c( 1, 0, 1, 0)
countSpliceKmers(sq, seqid, lEnd, rStart, width, strand, k=2)
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