testBaseline - Two-sided test of BASELINe PDFs

Description

testBaseline performs a two-sample significance test of BASELINe posterior probability density functions (PDFs).

Usage

testBaseline(baseline, groupBy)

Arguments

baseline
Baseline object containing the db and grouped BASELINe PDFs returned by groupBaseline.
groupBy
string defining the column in the db slot of the Baseline containing sequence or group identifiers.

Value

A data.frame with test results containing the following columns:

  • region: sequence region, such as cdr and fwr.
  • test: string defining the groups be compared. The string is formatted as the conclusion associated with the p-value in the form GROUP1 != GROUP2. Meaning, the p-value for rejection of the null hypothesis that GROUP1 and GROUP2 have equivalent distributions.
  • pvalue: two-sided p-value for the comparison.
  • fdr: FDR corrected pvalue.

References

  1. Yaari G, et al. Quantifying selection in high-throughput immunoglobulin sequencing data sets. Nucleic Acids Res. 2012 40(17):e134. (Corrections at http://selection.med.yale.edu/baseline/correction/)

Examples

# Subset example data as a demo
data(ExampleDb, package="alakazam")
db <- subset(ExampleDb, c_call %in% c("IGHM", "IGHG"))
set.seed(112)
db <- dplyr::slice_sample(db, n=200)

# 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)

calcBaseline will calculate observed and expected mutations for clonal_sequence using clonal_germline as a reference.

Calculating BASELINe probability density functions...



# Group PDFs by the isotype
grouped <- groupBaseline(baseline, groupBy="c_call")


Grouping BASELINe probability density functions...
Calculating BASELINe statistics...



# Visualize isotype PDFs
plot(grouped, "c_call")

7


# Perform test on isotype PDFs
testBaseline(grouped, groupBy="c_call")

  region         test    pvalue       fdr
1    cdr IGHM != IGHG 0.1353078 0.1353078
2    fwr IGHM != IGHG 0.1112142 0.1353078

See also

To generate the Baseline input object see groupBaseline.