shazam (version 0.1.4)

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
data(ExampleDb, package="alakazam")
db <- subset(ExampleDb, ISOTYPE %in% c("IgA", "IgG") & SAMPLE == "+7d")

# Calculate BASELINe
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 isotype and sample annotations.
grouped <- groupBaseline(baseline, groupBy=c("SAMPLE", "ISOTYPE"))

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