shazam (version 0.1.2)

getBaselineStats: Gets the summary statistics of a Baseline object

Description

getBaselineStats is an accessor method that returns the summary statistics data.frame stored in the stats slot of a Baseline object - provided groupBaseline has already been run.

Usage

getBaselineStats(baseline)

Arguments

baseline

Baseline object that has been run through either groupBaseline or summarizeBaseline.

Value

A data.frame with the BASELINe selection strength scores (Sigma), 95% confidence intervals and P-values.

See Also

For calculating the BASELINe summary statistics see summarizeBaseline.

Examples

# Subset example data
db <- subset(InfluenzaDb, CPRIMER %in% c("IGHA","IGHM") & 
                          BARCODE %in% c("RL016","RL018","RL019","RL021"))

# Calculate BASELINe
# By default, calcBaseline collapses the sequences in the db by the column "CLONE",
# calculates the numbers of observed mutations and expected frequencies of mutations,
# as defined in the IMGT_V_NO_CDR3 and using the HS5FModel targeting model.
# Then, it calculates  the BASELINe posterior probability density functions (PDFs) for
# sequences in the updated db files; using the focused test statistic
db_baseline <- calcBaseline(db, 
                            sequenceColumn="SEQUENCE_IMGT",
                            germlineColumn="GERMLINE_IMGT_D_MASK", 
                            testStatistic="focused",
                            regionDefinition=IMGT_V_NO_CDR3,
                            targetingModel = HS5FModel,
                            nproc = 1)

# Grouping the PDFs by the BARCODE and CPRIMER columns in the db, corresponding 
# respectively to sample barcodes and the constant region isotype primers.
baseline_group <- groupBaseline(db_baseline, groupBy=c("BARCODE", "CPRIMER"))

# Get a data.frame of the summary statistics
getBaselineStats(baseline_group)