upload.datatable.to.database: upload.datatable.to.database

In decusInLabore/biologicSeqTools2: Seq Analysis Helper Functions

upload.datatable.to.database

Description

mode options: SQLite, MySQL

Usage

upload.datatable.to.database(
  host = NULL,
  port = 6008,
  user = NULL,
  password = NULL,
  prim.data.db = "project.database",
  dbTableName = "rnaseqdbTableName",
  df.data = "df.data.to.upload",
  db.col.parameter.list =
    list(`VARCHAR(255) CHARACTER SET latin1 COLLATE latin1_swedish_ci` =
    c("gene_description"), `VARCHAR(50) CHARACTER SET latin1 COLLATE latin1_swedish_ci` =
    c("ENSG", "ENSMUSG", "hgnc_symbol", "mgi_symbol", "uniprot", "entrezgene",
    "display_ptm", "^sequence_window", "p_site_env", "for_GSEA_gene_chip",
    "associated_gene_name", "gene_type"),
    `VARCHAR(1) CHARACTER SET latin1 COLLATE latin1_swedish_ci` = c("ppos", "amino_acid",
    "charge", "known_site"), `BIGINT(8) NULL DEFAULT NULL` = c("row_names"),
    `INT(8) NULL DEFAULT NULL` = c("row_id", 
     "cluster_order", "cluster_id",
    "count_cut_off", "^position$", "raw_counts"), `DECIMAL(6,3) NULL DEFAULT NULL` =
    c("norm_counts", "NES", "logFC", "lg2_avg", "intensity", "^int", "iBAQ",
    "^localization_prob$"), `DECIMAL(6,5) NULL DEFAULT NULL` = c("padj", "pvalue",
    "^pep$")),
  increment = 5000,
  new.table = FALSE,
  first.row.name.index = 1,
  startOnlyWithConnectionCount1 = FALSE,
  cols2Index = NULL,
  indexName = NULL,
  mode = "MySQL",
  addRowNamesColumn = TRUE
)

Arguments

host	URL or IP address of the database server. NULL if mode is SQLite
user	database user name. Needs privileges for INSERT, DELETE, DROP and SELECT
password	database password
prim.data.db	primary database name
dbTableName	Name of the database table to upload
df.data	data.frame to upload to the database
db.col.parameter.list	This list specifies the category for a database column. This ideally is filled using the function inferDbColumns(dbTableName)
increment	= 5000,
new.table	= FALSE,
first.row.name.index	= 1,
startOnlyWithConnectionCount1	= FALSE,
cols2Index	= NULL,
mode	= "MySQL"

decusInLabore/biologicSeqTools2 documentation built on Nov. 21, 2024, 9:04 p.m.