collapseClones() returns NAs in CLONAL_SEQUENCE

[Julian Zhou]

When expandedDb = T, $CLONAL_SEQUENCE contains mostly NAs (not supposed to be).

Reproducible example using the same Example code provided by the package:

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

# Build clonal consensus for V region
db_new <- collapseClones(db, cloneColumn="CLONE", 
                        sequenceColumn="SEQUENCE_IMGT",
                        germlineColumn="GERMLINE_IMGT_D_MASK",
                        regionDefinition=IMGT_V_NO_CDR3,
                        nproc=1,
                        expandedDb = T) # this line is the only difference compared to Example

# See the NA problem
sum(is.na(db_new$CLONAL_S))

[Jason Vander Heiden]

Hrm. From:

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

# Build clonal consensus for V region
db_new <- collapseClones(db, cloneColumn="CLONE", 
                        sequenceColumn="SEQUENCE_IMGT",
                        germlineColumn="GERMLINE_IMGT_D_MASK",
                        regionDefinition=IMGT_V_NO_CDR3,
                        nproc=1,
                        expandedDb = T) # this line is the only difference compared to Example

# See the NA problem
sum(is.na(db_new$CLONAL_SEQUENCE))

I get:

[1] 0

Rebuild maybe?

[Julian Zhou]

FALSE ALARM :O

[Jason Vander Heiden]

Invalid!