Add2DB {DECIPHER} | R Documentation |
Adds a data.frame
to a database table by its row.names
.
Add2DB(myData, dbFile, tblName = "Seqs", clause = "", verbose = TRUE)
myData |
Data frame containing information to be added to the |
dbFile |
A SQLite connection object or a character string specifying the path to the database file. |
tblName |
Character string specifying the table in which to add the data. |
clause |
An optional character string to append to the query as part of a “where clause”. |
verbose |
Logical indicating whether to display each query as it is sent to the database. |
Data contained in myData
will be added to the tblName
by its respective row.names
.
Returns TRUE
if the data was added successfully, or FALSE
otherwise.
Erik Wright eswright@pitt.edu
ES Wright (2016) "Using DECIPHER v2.0 to Analyze Big Biological Sequence Data in R". The R Journal, 8(1), 352-359.
# Create a sequence database gen <- system.file("extdata", "Bacteria_175seqs.gen", package="DECIPHER") dbConn <- dbConnect(SQLite(), ":memory:") Seqs2DB(gen, "GenBank", dbConn, "Bacteria") # Identify the sequence lengths l <- IdLengths(dbConn) # Add lengths to the database Add2DB(l, dbConn) # View the added lengths BrowseDB(dbConn) # Change the value of existing columns ids <- data.frame(identifier=rep("Bacteroidetes", 18), stringsAsFactors=FALSE) rownames(ids) <- 10:27 Add2DB(ids, dbConn) BrowseDB(dbConn) # Add data to a subset of rows using a clause ids[[1]][] <- "Changed" nrow(ids) # 18 rows Add2DB(ids, dbConn, clause="accession like 'EU808318%'") BrowseDB(dbConn) # only 1 row effected dbDisconnect(dbConn)