seqTools (version 1.6.0)

countSpliceKmers: 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).

Usage

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

Arguments

dna

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 !)

Value

.

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.

Examples

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)