reconcile_sample_name: Partial name matching in datasource.

Description Usage Arguments Value Author(s) See Also Examples

Description

Provides a simple mechanism to decipher a user-specified sample ID based on the specified columns and table in the priorDbParams object. Matching is performed in the sense of grep so at least a unique substring should be specified in sample.id.

Usage

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reconcile.sample.name(sample.id, db.con, param.obj)

Arguments

sample.id

A character vector of length 1 containing the value to use for the sample ID matching.

db.con

An object that inherits from DBIConnection, for example a MySQLConnection object.

param.obj

A priorDbParams object.

Value

A list containing three elements:

recon

The reconciled sample ID, usually a character string

ind

The unique index of the sample ID, usually an integer

num.pats

The total number of samples in the datasource

Author(s)

Daniel Bottomly

See Also

priorDbParams, dbConnect

Examples

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if(require(RSQLite) && require(HitWalkerData))
{
  data(params)
  db.con <- dbConnect("SQLite", hitwalker.db.path())
  sample.id.list <- reconcile.sample.name("08-00102", db.con, examp.prior.param)
  dbDisconnect(db.con)
}

dbottomly/HitWalker documentation built on May 15, 2019, 1:22 a.m.