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 and windowSize 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.