| 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)