countSpliceKmers: countSpliceKmers: Counting K-mers on donor (5', upstream)...
In seqTools: Analysis of nucleotide, sequence and quality content on fastq files.

Description Usage Arguments Details Value Author(s) Examples

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).

1	countSpliceKmers(dna,seqid,lEnd,rStart,width,strand,k)

`dna`	`character`. Vector of DNA sequences. `dna` must not contain other characters as "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!)

The function returns a matrix. Each colum containts 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.

matrix.

Wolfgang Kaisers

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)