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.

Examples

# 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)

Calculating the expected frequencies of mutations...
Calculating BASELINe probability density functions...


# Edit the field "description"
baseline <- editBaseline(baseline, field_name="description", 
value="+7d IgA & IgG")

See also

See Baseline for the return object.