shazam (version 0.1.9)

editBaseline: Edit the Baseline object

Description

editBaseline edits a field in a Baseline object.

Usage

editBaseline(baseline, field_name, value)

Arguments

baseline

The Baseline S4 object to be edited.

field_name

Name of the field in the Baseline S4 object to be edited.

value

The value to set the field_name.

Value

A Baseline object with the field of choice updated.

See Also

See Baseline for the return object.

Examples

# NOT RUN {
# Subset example data
data(ExampleDb, package="alakazam")
db <- subset(ExampleDb, ISOTYPE %in% c("IgA", "IgG") & SAMPLE == "+7d")

# Collapse clones
db <- collapseClones(db, sequenceColumn="SEQUENCE_IMGT",
                     germlineColumn="GERMLINE_IMGT_D_MASK",
                     method="thresholdedFreq", minimumFrequency=0.6,
                     includeAmbiguous=FALSE, breakTiesStochastic=FALSE)
                     
# Calculate BASELINe
baseline <- calcBaseline(db, 
                         sequenceColumn="SEQUENCE_IMGT",
                         germlineColumn="GERMLINE_IMGT_D_MASK", 
                         testStatistic="focused",
                         regionDefinition=IMGT_V,
                         targetingModel=HH_S5F,
                         nproc=1)
                         
# Edit the field "description"
baseline <- editBaseline(baseline, field_name="description", 
                         value="+7d IgA & IgG")
                                                  
# }