testBaseline: Two-sided test of BASELINe PDFs

In shazam: Immunoglobulin Somatic Hypermutation Analysis

Two-sided test of BASELINe PDFs

Description

testBaseline performs a two-sample signifance 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 formated 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. (Corretions at http://selection.med.yale.edu/baseline/correction/)

See Also

To generate the Baseline input object see groupBaseline.

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)

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

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

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

shazam documentation built on Oct. 3, 2023, 1:06 a.m.