R: countSpliceKmers: Counting K-mers on donor (5', upstream)...
countSpliceKmers
R Documentation
countSpliceKmers: Counting K-mers on donor (5', upstream) sides
(exonic) of splice sites.
Description
The function regards the given string as DNA sequence bearing a collection of
splice sites. The given 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).
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.
seqid
numeric. Vector of (1-based) values coding for one
of the given sequences.
lEnd
numeric. Vector of (1-based) left-end positions.
Will be used as rightmost window position.
rStart
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).
width
numeric. Vector of window width values.
strand
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.
k
numeric. Number of nucleotides in tabled DNA motifs.
Only a single value is allowed (length(n) = 1 !)
Details
The function returns a matrix.
Each colum contains the motif-count values for one frame.
Each row represents one DNA motif.
The DNA sequence of the DNA motif is given as row.name.