slideWindowSeq - Sliding window approach towards filtering a single sequence
Description¶
slideWindowSeq
determines whether an input sequence contains equal to or more than
a given number of mutations in a given length of consecutive nucleotides (a “window”)
when compared to a germline sequence.
Usage¶
slideWindowSeq(inputSeq, germlineSeq, mutThresh, windowSize)
Arguments¶
- inputSeq
- input sequence.
- germlineSeq
- germline sequence.
- mutThresh
- threshold on the number of mutations in
windowSize
consecutive nucleotides. Must be between 1 andwindowSize
inclusive. - windowSize
- length of consecutive nucleotides. Must be at least 2.
Value¶
TRUE
if there are equal to or more than mutThresh
number of mutations
in any window of windowSize
consecutive nucleotides (i.e. the sequence should
be filtered); FALSE
if otherwise.
Examples¶
# Use an entry in the example data for input and germline sequence
data(ExampleDb, package="alakazam")
in_seq <- ExampleDb[["sequence_alignment"]][100]
germ_seq <- ExampleDb[["germline_alignment_d_mask"]][100]
# Determine if in_seq has 6 or more mutations in 10 consecutive nucleotides
slideWindowSeq(inputSeq=in_seq, germlineSeq=germ_seq, mutThresh=6, windowSize=10)
[1] FALSE
slideWindowSeq(inputSeq="TCGTCGAAAA", germlineSeq="AAAAAAAAAA", mutThresh=6, windowSize=10)
[1] FALSE
See also¶
calcObservedMutations is called by slideWindowSeq
to identify observed
mutations. See slideWindowDb for applying the sliding window approach on a
data.frame
. See slideWindowTune for parameter tuning for mutThresh
and windowSize
.