sqlForge-popDB: Populates an SQLite DB with and produces a schema definition

Description Usage Arguments Examples

Description

Creates SQLite file useful for making a SQLite based annotation package. Also produces the schema file which details the schema for the database produced.

Usage

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   populateDB(schema, ...)

#  usage case with required arguments
#  populateDB(schema, prefix, chipSrc, metaDataSrc)

#  usage case with all possible arguments
#  populateDB(schema, affy, prefix, fileName, chipMapSrc, chipSrc,
#  metaDataSrc, otherSrc, baseMapType, outputDir, printSchema)

Arguments

schema

String listing the schema that you want to use to make the DB. You can list schemas with available.dbschemas()

affy

Boolean to indicate if this is starting from an affy csv file or not. If it is, then that will be parsed to make the sqlite file, if not, then you can feed a tab delimited file with IDs as was done before with AnnBuilder.

prefix

prefix is the first part of the eventual desired package name. (ie. "prefix.sqlite")

fileName

The path and filename for the mapping file to be parsed. This can either be an affy csv file or it can be a more classic file type. This is only needed when making chip packages.

chipMapSrc

The path and filename to the intermediate database containing the mapping data for allowed ID types and how these IDs relate to each other. If not provided, then the appropriate source DB from the most current .db0 package will be used instead.

chipSrc

The path and filename to the intermediate database containing the annotation data for the sqlite to build. If not provided, then the appropriate source DB from the most current .db0 package will be used instead.

metaDataSrc

Either a named character vector containing pertinent information about the metadata OR the path and filename to the intermediate database containing the metadata information for the package.

If this is a custom package, then it must be a named vector with the following fields:

metaDataSrc <- c( DBSCHEMA="the DB schema", ORGANISM="the organism", SPECIES="the species", MANUFACTURER="the manufacturer", CHIPNAME="the chipName", MANUFACTURERURL="the manufacturerUrl")

otherSrc

The path and filenames to any other lists of IDs which might add information about how a probe will map.

baseMapType

The type of ID that is used for the initial base mapping. If using a classic base mapping file, this should be the ID type present in the fileName. This can be any of the following values: "gb" = for genbank IDs "ug" = unigene IDs "eg" = Entrez Gene IDs "refseq" = refseq IDs "gbNRef" = mixture of genbank and refseq IDs

outputDir

Where you would like the output files to be placed.

printSchema

Boolean to indicate whether or not to produce an output of the schema (default is FALSE).

...

Just used so we can have a wrapper function. Ignore this argument.

Examples

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## Not run: 
  ##Set up the metadata
  my_metaDataSrc <- c( DBSCHEMA="the DB schema",
                    ORGANISM="the organism",
                    SPECIES="the species",
                    MANUFACTURER="the manufacturer",
                    CHIPNAME="the chipName",
                    MANUFACTURERURL="the manufacturerUrl")  

  ##Builds the org.Hs.eg sqlite:
  populateDB(
    "HUMAN_DB",
    prefix="org.Hs.eg",
    chipSrc = "~/proj/mcarlson/sqliteGen/annosrc/db/chipsrc_human.sqlite",
    metaDataSrc = my_metaDataSrc,
    printSchema=TRUE)


  ##Builds hgu95av2.sqlite:
  populateDB(
      "HUMANCHIP_DB",
      affy=TRUE,
      prefix="hgu95av2",
      fileName="~/proj/mcarlson/sqliteGen/srcFiles/hgu95av2/HG_U95Av2.na27.annot.csv",
      metaDataSrc=my_metaDataSrc,
      baseMapType="gbNRef")


  ##Builds the ag.sqlite:
  populateDB("ARABIDOPSISCHIP_DB",
             affy=TRUE,
             prefix="ag",
             metaDataSrc=my_metaDataSrc)


  ##Builds yeast2.sqlite:  
  populateDB(
      "YEASTCHIP_DB",
      affy=TRUE,
      prefix="yeast2",
      fileName="~/proj/mcarlson/sqliteGen/srcFiles/yeast2/Yeast_2.na27.annot.csv",
      metaDataSrc=metaDataSrc)


## End(Not run)

AnnotationForge documentation built on Aug. 6, 2018, 2 a.m.