shazam (version 1.2.0)

calcBaseline: Calculate the BASELINe PDFs (including for regions that include CDR3 and FWR4)

Description

calcBaseline calculates the BASELINe posterior probability density functions (PDFs) for sequences in the given Change-O data.frame.

Usage

calcBaseline(
  db,
  sequenceColumn = "clonal_sequence",
  germlineColumn = "clonal_germline",
  testStatistic = c("local", "focused", "imbalanced"),
  regionDefinition = NULL,
  targetingModel = HH_S5F,
  mutationDefinition = NULL,
  calcStats = FALSE,
  nproc = 1,
  cloneColumn = NULL,
  juncLengthColumn = NULL
)

Value

A Baseline object containing the modified db and BASELINe posterior probability density functions (PDF) for each of the sequences.

Arguments

db

data.frame containing sequence data and annotations.

sequenceColumn

character name of the column in db containing input sequences.

germlineColumn

character name of the column in db containing germline sequences.

testStatistic

character indicating the statistical framework used to test for selection. One of c("local", "focused", "imbalanced").

regionDefinition

RegionDefinition object defining the regions and boundaries of the Ig sequences.

targetingModel

TargetingModel object. Default is HH_S5F.

mutationDefinition

MutationDefinition object defining replacement and silent mutation criteria. If NULL then replacement and silent are determined by exact amino acid identity. Note, if the input data.frame already contains observed and expected mutation frequency columns then mutations will not be recalculated and this argument will be ignored.

calcStats

logical indicating whether or not to calculate the summary statistics data.frame stored in the stats slot of a Baseline object.

nproc

number of cores to distribute the operation over. If nproc=0 then the cluster has already been set and will not be reset.

cloneColumn

character name of the column in db containing clonal identifiers. Relevant only for when regionDefinition includes CDR and FWR4 (else this value can be NULL)

juncLengthColumn

character name of the column in db containing the junction length. Relevant only for when regionDefinition includes CDR and FWR4 (else this value can be NULL)

Details

Calculates the BASELINe posterior probability density function (PDF) for sequences in the provided db.

Note: Individual sequences within clonal groups are not, strictly speaking, independent events and it is generally appropriate to only analyze selection pressures on an effective sequence for each clonal group. For this reason, it is strongly recommended that the input db contains one effective sequence per clone. Effective clonal sequences can be obtained by calling the collapseClones function.

If the db does not contain the required columns to calculate the PDFs (namely mu_count & mu_expected) then the function will:

1. Calculate the numbers of observed mutations.

2. Calculate the expected frequencies of mutations and modify the provided db. The modified db will be included as part of the returned Baseline object.

The testStatistic indicates the statistical framework used to test for selection. E.g.

• local = CDR_R / (CDR_R + CDR_S).

• focused = CDR_R / (CDR_R + CDR_S + FWR_S).

• imbalanced = CDR_R + CDR_S / (CDR_R + CDR_S + FWR_S + FRW_R).

For focused the regionDefinition must only contain two regions. If more than two regions are defined the local test statistic will be used. For further information on the frame of these tests see Uduman et al. (2011).

References

1. Hershberg U, et al. Improved methods for detecting selection by mutation analysis of Ig V region sequences. Int Immunol. 2008 20(5):683-94.

2. Uduman M, et al. Detecting selection in immunoglobulin sequences. Nucleic Acids Res. 2011 39(Web Server issue):W499-504.

3. Yaari G, et al. Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput immunoglobulin sequencing data. Front Immunol. 2013 4(November):358.

See Also

See Baseline for the return object. See groupBaseline and summarizeBaseline for further processing. See plotBaselineSummary and plotBaselineDensity for plotting results.

Examples

# Load and subset example data
data(ExampleDb, package="alakazam")
db <- subset(ExampleDb, c_call == "IGHG" & sample_id == "+7d")

# Collapse clones
db <- collapseClones(db, cloneColumn="clone_id", 
                     sequenceColumn="sequence_alignment",
                     germlineColumn="germline_alignment_d_mask",
                     method="thresholdedFreq", minimumFrequency=0.6,
                     includeAmbiguous=FALSE, breakTiesStochastic=FALSE)
 
# Calculate BASELINe
baseline <- calcBaseline(db, 
                         sequenceColumn="clonal_sequence",
                         germlineColumn="clonal_germline", 
                         testStatistic="focused",
                         regionDefinition=IMGT_V,
                         targetingModel=HH_S5F,
                         nproc=1)