
data.frame
slideWindowDb
determines whether each input sequence in a data.frame
contains equal to or more than a given number of mutations in a given length of
consecutive nucleotides (a "window") when compared to their respective germline
sequence.
slideWindowDb(db, sequenceColumn = "SEQUENCE_IMGT",
germlineColumn = "GERMLINE_IMGT_D_MASK", mutThresh, windowSize)
data.frame
containing sequence data.
name of the column containing IMGT-gapped sample sequences.
name of the column containing IMGT-gapped germline sequences.
threshold on the number of mutations in windowSize
consecutive nucleotides. Must be between 1 and windowSize
inclusive.
length of consecutive nucleotides. Must be at least 2.
a logical vector. The length of the vector matches the number of input sequences in
db
. Each entry in the vector indicates whether the corresponding input sequence
should be filtered based on the given parameters.
See slideWindowSeq for applying the sliding window approach on a single sequence.
See slideWindowTune for parameter tuning for mutThresh
and windowSize
.
# NOT RUN {
# Use an entry in the example data for input and germline sequence
data(ExampleDb, package="alakazam")
# Apply the sliding window approach on a subset of ExampleDb
slideWindowDb(db = ExampleDb[1:10, ], mutThresh=6, windowSize=10)
# }
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