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, returnRaw = FALSE)

Arguments

inputSeq
input sequence.
germlineSeq
germline sequence.
frequency
logical indicating whether or not to calculate mutation frequencies. The denominator used is the number of bases that are non-N in both the input and the germline sequences. 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.
returnRaw
return the positions of point mutations and their corresponding mutation types, as opposed to counts of mutations. Also returns the number of non-N bases used as the denominator when calculating frequency. Default is FALSE.

Value

For returnRaw=FALSE, an array with the number of replacement (R) and silent(S) mutations. For returnRaw=TRUE, a list containing a data frame ($pos) whose columns (position, type, and region) indicate the position, mutation type (R or S), and region of each mutation; and a vector ($nonN) indicating the number of non-N bases in regions defined by regionDefinition.

Details

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

Note that only replacement (R) and silent (S) mutations are included in the results. Stop mutations and mutations such as the case in which NNN in the germline sequence is observed as NNC in the input sequence are excluded. In other words, a result that is NA or zero indicates absence of R and S mutations, not necessarily all types of mutations, such as the excluded ones mentioned above.

Examples

# Use an entry in the example data for input and germline sequence
data(ExampleDb, package="alakazam")
in_seq <- ExampleDb[100, "SEQUENCE_IMGT"]
germ_seq <-  ExampleDb[100, "GERMLINE_IMGT_D_MASK"]

# Identify all mutations in the sequence
ex1_raw = calcObservedMutations(in_seq, germ_seq, returnRaw=TRUE)
# Count all mutations in the sequence
ex1_count = calcObservedMutations(in_seq, germ_seq, returnRaw=FALSE)
ex1_freq = calcObservedMutations(in_seq, germ_seq, returnRaw=FALSE, frequency=TRUE)
# Compare this with ex1_count
table(ex1_raw$pos$region, ex1_raw$pos$type)


       R  S
  SEQ 11  7

# Compare this with ex1_freq
table(ex1_raw$pos$region, ex1_raw$pos$type) / ex1_raw$nonN


               R          S
  SEQ 0.03353659 0.02134146


# Identify only mutations the V segment minus CDR3
ex2_raw = calcObservedMutations(in_seq, germ_seq, 
regionDefinition=IMGT_V, returnRaw=TRUE)
# Count only mutations the V segment minus CDR3
ex2_count = calcObservedMutations(in_seq, germ_seq, 
regionDefinition=IMGT_V, returnRaw=FALSE)
ex2_freq = calcObservedMutations(in_seq, germ_seq, 
regionDefinition=IMGT_V, returnRaw=FALSE,
frequency=TRUE)
# Compare this with ex2_count
table(ex2_raw$pos$region, ex2_raw$pos$type)                                 


      R S
  CDR 4 1
  FWR 7 4

# Compare this with ex2_freq
table(ex2_raw$pos$region, ex2_raw$pos$type) / ex2_raw$nonN                                        


               R          S
  CDR 0.08333333 0.02083333
  FWR 0.02916667 0.01666667


# Identify mutations by change in hydropathy class
ex3_raw = calcObservedMutations(in_seq, germ_seq, regionDefinition=IMGT_V,
mutationDefinition=HYDROPATHY_MUTATIONS, returnRaw=TRUE)
# Count mutations by change in hydropathy class
ex3_count = calcObservedMutations(in_seq, germ_seq, regionDefinition=IMGT_V,
mutationDefinition=HYDROPATHY_MUTATIONS, returnRaw=FALSE)
ex3_freq = calcObservedMutations(in_seq, germ_seq, regionDefinition=IMGT_V,
mutationDefinition=HYDROPATHY_MUTATIONS, returnRaw=FALSE, 
frequency=TRUE)
# Compre this with ex3_count
table(ex3_raw$pos$region, ex3_raw$pos$type)                                        


      R S
  CDR 3 2
  FWR 4 7

# Compare this with ex3_freq
table(ex3_raw$pos$region, ex3_raw$pos$type) / ex3_raw$nonN

               R          S
  CDR 0.06250000 0.04166667
  FWR 0.01666667 0.02916667

See also

See observedMutations for counting the number of observed mutations in a data.frame.