calcObservedMutations: Count the number of observed mutations in a sequence.

Description

calcObservedMutations determines all the mutations in a given input seqeunce compared to its germline sequence.

Usage

calcObservedMutations(inputSeq, germlineSeq, frequency = FALSE, regionDefinition = NULL, mutationDefinition = NULL)

Arguments

inputSeq

input sequence.

germlineSeq

germline sequence.

frequency

logical indicating whether or not to calculate mutation frequencies. Default is FALSE.

regionDefinition

RegionDefinition object defining the regions and boundaries of the Ig sequences. Note, only the part of sequences defined in regionDefinition are analyzed. If NULL, mutations are counted for entire sequence.

mutationDefinition

MutationDefinition object defining replacement and silent mutation criteria. If NULL then replacement and silent are determined by exact amino acid identity.

Value

An array of the mutations, replacement (R) or silent(S), with the names indicating the nucleotide postion of the mutations in the sequence.

Details

Each mutation is considered independently in its codon context. Note, only the part of inputSeq defined in regionDefinition is analyzed. For example, when using the default IMGT_V_NO_CDR3 definition, then mutations in positions beyond 312 will be ignored.

Examples

Run this code

# Extracting the first entry in the example data to use for input and germline sequences.
inputSeq <- InfluenzaDb[1, "SEQUENCE_IMGT"]
germlineSeq <-  InfluenzaDb[1, "GERMLINE_IMGT_D_MASK"]

# Identify all mutations in the sequence
calcObservedMutations(inputSeq, germlineSeq)

# Identify only mutations the V segment minus CDR3
calcObservedMutations(inputSeq, germlineSeq, regionDefinition=IMGT_V_NO_CDR3)
 
# Identify mutations by change in hydropathy class
calcObservedMutations(inputSeq, germlineSeq, regionDefinition=IMGT_V_NO_CDR3,
                      mutationDefinition=HYDROPATHY_MUTATIONS, frequency=TRUE)