- changed status to resolved
calcBaseline, error when no clones to collapse
Issue #67
resolved
If the db file has the field clone, and the clone ids are unique, calcBaseline throws the error:
Collapsing clonal sequences... Error in cons_mat[2, ] : subscript out of bounds
Reproduce:
library(shazam)
data(ExampleDb, package="alakazam")
db <- subset(ExampleDb, ISOTYPE %in% c("IgA", "IgG") & SAMPLE == "+7d")
db <- db[1:10,]
db$CLONE <- 1:10
baseline <- calcBaseline(db,
sequenceColumn="SEQUENCE_IMGT",
germlineColumn="GERMLINE_IMGT_D_MASK",
testStatistic="focused",
regionDefinition=IMGT_V_NO_CDR3,
targetingModel = HS5FModel,
nproc=1)
Comments (1)
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Dumb. Fixed in b94c96a.