Description Usage Arguments Details Value Author(s) See Also Examples
Agglomerates sequences into groups within a certain size range based on taxonomic rank.
1 2 3 4 5 6 7 | FormGroups(dbFile,
tblName = "Seqs",
goalSize = 50,
minGroupSize = 25,
maxGroupSize = 500,
add2tbl = FALSE,
verbose = TRUE)
|
dbFile |
A SQLite connection object or a character string specifying the path to the database file. |
tblName |
Character string specifying the table where the rank information is located. |
goalSize |
Number of sequences required in each group to stop adding more sequences. |
minGroupSize |
Minimum number of sequences in each group required to stop trying to recombine with a larger group. |
maxGroupSize |
Maximum number of sequences in each group allowed to continue agglomeration. |
add2tbl |
Logical or a character string specifying the table name in which to add the result. |
verbose |
Logical indicating whether to print database queries and other information. |
FormGroups
uses the “rank” field in the dbFile
table to group sequences with similar taxonomic rank. Rank information must be present in the tblName
, such as that created by default when importing sequences from a GenBank formatted file.
Beginning with the least common ranks, the algorithm agglomerates groups with similar ranks until the goalSize
is reached. If the group size is below minGroupSize
then further agglomeration is attempted with a larger group. If additional agglomeration results in a group larger than maxGroupSize
then the agglomeration is undone so that the group is smaller.
A data.frame
with the rank
and corresponding group name as identifier
. Note that quotes are stripped from group names to prevent problems that they may cause. The origin
gives the rank
preceding the identifier
. If add2tbl
is not FALSE
then the “identifier” and “origin” columns are updated in dbFile
.
Erik Wright [email protected]
1 2 3 | db <- system.file("extdata", "Bacteria_175seqs.sqlite", package="DECIPHER")
g <- FormGroups(db, goalSize=10, minGroupSize=5, maxGroupSize=20)
head(g)
|
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