[Gtdb-commits] r30 - in pkg/gt.db: R demo inst/schema man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Feb 16 20:35:51 CET 2010
Author: dahinds
Date: 2010-02-16 20:35:51 +0100 (Tue, 16 Feb 2010)
New Revision: 30
Removed:
pkg/gt.db/man/ls.assay.group.Rd
pkg/gt.db/man/mk.assay.group.Rd
Modified:
pkg/gt.db/R/admin.R
pkg/gt.db/R/assay.R
pkg/gt.db/R/rawdata.R
pkg/gt.db/demo/setup.gt.demo.R
pkg/gt.db/inst/schema/mk_mysql.sql
pkg/gt.db/inst/schema/mk_oracle.sql
pkg/gt.db/inst/schema/mk_sqlite.sql
pkg/gt.db/inst/schema/rm_mysql.sql
pkg/gt.db/inst/schema/rm_oracle.sql
pkg/gt.db/inst/schema/rm_sqlite.sql
pkg/gt.db/man/ls.assay.Rd
pkg/gt.db/man/ls.platform.Rd
pkg/gt.db/man/mk.assay.Rd
pkg/gt.db/man/mk.platform.Rd
Log:
- removed 'assay group' from schema, removed support
- introduced low level support for a flag word for assays
Modified: pkg/gt.db/R/admin.R
===================================================================
--- pkg/gt.db/R/admin.R 2010-02-13 08:37:31 UTC (rev 29)
+++ pkg/gt.db/R/admin.R 2010-02-16 19:35:51 UTC (rev 30)
@@ -62,8 +62,6 @@
{
sql <-
"select platform_id, name platform_name, description,
- (select count(*) from assay_group g
- where p.platform_id=g.platform_id) assay_groups,
(select count(*) from dataset d
where p.platform_id=d.platform_id) datasets,
created_by, created_dt
Modified: pkg/gt.db/R/assay.R
===================================================================
--- pkg/gt.db/R/assay.R 2010-02-13 08:37:31 UTC (rev 29)
+++ pkg/gt.db/R/assay.R 2010-02-16 19:35:51 UTC (rev 30)
@@ -70,63 +70,26 @@
#---------------------------------------------------------------------
-ls.assay.group <- function(platform.name, show.ids=FALSE)
+ls.assay <- function(platform.name, show.ids=FALSE)
{
sql <-
- 'select assay_group_id, name assay_group,
- description, created_by, created_dt
- from assay_group where platform_id=:1'
+ 'select assay_id, name assay_name, alleles, probe_seq
+ from assay where platform_id=:1'
r <- sql.query(gt.db::.gt.db, sql, lookup.id('platform', platform.name))
- .filter.ids(r, show.ids)
-}
-
-mk.assay.group <-
-function(platform.name, assay.group, description)
-{
- .check.name(assay.group)
- plat.id <- lookup.id('platform', platform.name)
- sql <-
- "insert into assay_group
- values (null, :1, :2, :3, :user:, :sysdate:)"
- sql.exec(gt.db::.gt.db, sql, plat.id, assay.group, description)
-}
-
-rm.assay.group <- function(platform.name, assay.group)
-{
- grp.id <- lookup.id('assay_group', assay.group,
- platform.id=lookup.id('platform', platform.name))
- sql <- 'delete from assay_group where assay_group_id=:1'
- sql.exec(gt.db::.gt.db, sql, grp.id)
-}
-
-#---------------------------------------------------------------------
-
-ls.assay <- function(platform.name, assay.group='%', show.ids=FALSE)
-{
- sql <-
- 'select g.assay_group_id, g.name assay_group,
- assay_id, a.name assay_name, alleles, probe_seq
- from assay_group g, assay a
- where g.assay_group_id=a.assay_group_id
- and g.platform_id=:1
- and g.name like :2'
- r <- sql.query(gt.db::.gt.db, sql, lookup.id('platform', platform.name),
- assay.group)
.filter.ids(data.frame(r, row.names=r$assay.name), show.ids)
}
mk.assay <- function(platform.name, data, progress=FALSE)
{
plat.id <- lookup.id('platform', platform.name)
- grp.id <- lookup.id('assay_group', unique(data$assay.group),
- platform.id=plat.id)
.check.name(data$assay.name)
r <- (regexpr('^[a-zA-Z]*_[a-zA-Z]*$', data$probe.seq) < 0)
if (any(r,na.rm=TRUE))
stop("invalid probe sequence(s)", call.=FALSE)
+ if (is.null(data$flags)) data$flags <- 0
sql <- 'insert into assay values (null,:1,:2,:3,:4,:5)'
- sql.exec(gt.db::.gt.db, sql, plat.id, grp.id[data$assay.group],
- data[c('assay.name','alleles','probe.seq')],
+ sql.exec(gt.db::.gt.db, sql, plat.id,
+ data[c('assay.name','flags','alleles','probe.seq')],
progress=progress)
}
Modified: pkg/gt.db/R/rawdata.R
===================================================================
--- pkg/gt.db/R/rawdata.R 2010-02-13 08:37:31 UTC (rev 29)
+++ pkg/gt.db/R/rawdata.R 2010-02-16 19:35:51 UTC (rev 30)
@@ -73,9 +73,9 @@
.pack.chpdata <- function(data)
{
- x <- writeBin(as.integer(256*data$log.ratio),
+ x <- writeBin(as.integer(round(256*data$log.ratio)),
raw(), size=2, endian='little')
- y <- writeBin(as.integer(256*data$strength),
+ y <- writeBin(as.integer(round(256*data$strength)),
raw(), size=2, endian='little')
z <- as.raw(data$forced.call)
dim(x) <- dim(y) <- c(2,nrow(data))
Modified: pkg/gt.db/demo/setup.gt.demo.R
===================================================================
--- pkg/gt.db/demo/setup.gt.demo.R 2010-02-13 08:37:31 UTC (rev 29)
+++ pkg/gt.db/demo/setup.gt.demo.R 2010-02-16 19:35:51 UTC (rev 30)
@@ -27,10 +27,6 @@
# describe the platform and dataset
mk.platform('Demo_Set_1', 'Demo 10K SNP Set')
-mk.assay.group('Demo_Set_1', 'Des01', 'Array 1 of 4')
-mk.assay.group('Demo_Set_1', 'Des02', 'Array 2 of 4')
-mk.assay.group('Demo_Set_1', 'Des03', 'Array 3 of 4')
-mk.assay.group('Demo_Set_1', 'Des04', 'Array 4 of 4')
mk.mapping('Demo_Set_1', 'Demo_Set_1_b36',
'Platform 1 Mapping to NCBI Build 36', 'ncbi_b36')
mk.dataset('Demo_1', 'Demo', 'Demo_Set_1', 'Demo (HapMap) Dataset #1')
@@ -51,7 +47,6 @@
# describe the platform and dataset
mk.platform('Demo_Set_2', 'Demo Chr21 SNPs')
-mk.assay.group('Demo_Set_2', 'Des11', 'Array 11')
mk.mapping('Demo_Set_2', 'Demo_Set_2_b36',
'Platform 2 Mapping to NCBI Build 36', 'ncbi_b36')
mk.dataset('Demo_2', 'Demo', 'Demo_Set_2',
Modified: pkg/gt.db/inst/schema/mk_mysql.sql
===================================================================
--- pkg/gt.db/inst/schema/mk_mysql.sql 2010-02-13 08:37:31 UTC (rev 29)
+++ pkg/gt.db/inst/schema/mk_mysql.sql 2010-02-16 19:35:51 UTC (rev 30)
@@ -1,5 +1,6 @@
--
-- Copyright (C) 2009, Perlegen Sciences, Inc.
+-- Copyright (C) 2010, 23andMe, Inc.
--
-- Written by David A. Hinds <dhinds at sonic.net>
--
@@ -30,46 +31,31 @@
created_dt datetime
);
-create table assay_group
+create table assay_flag
(
- assay_group_id integer auto_increment primary key,
platform_id integer not null,
- name varchar(64) unique not null,
+ position integer not null,
+ name varchar(64) not null,
description varchar(255),
created_by varchar(64),
created_dt datetime,
+ constraint af_pk primary key (platform_id, position),
+ constraint af_uniq unique (platform_id, name),
foreign key (platform_id)
references platform(platform_id) on delete cascade
);
--- create table assay_flag
--- (
--- platform_id integer not null,
--- position integer not null,
--- name varchar(64) not null,
--- description varchar(255),
--- created_by varchar(64),
--- created_dt datetime,
--- constraint af_pk primary key (platform_id, position),
--- constraint af_uniq unique (platform_id, name),
--- foreign key (platform_id)
--- references platform(platform_id) on delete cascade
--- );
-
create table assay
(
assay_id integer auto_increment primary key,
platform_id integer not null,
- assay_group_id integer not null,
name varchar(255) not null,
- -- flags integer,
+ flags integer,
alleles varchar(255),
probe_seq varchar(255),
constraint assay_uniq unique (platform_id, name),
foreign key (platform_id)
- references platform(platform_id) on delete cascade,
- foreign key (assay_group_id)
- references assay_group(assay_group_id) on delete cascade
+ references platform(platform_id) on delete cascade
);
create table mapping
Modified: pkg/gt.db/inst/schema/mk_oracle.sql
===================================================================
--- pkg/gt.db/inst/schema/mk_oracle.sql 2010-02-13 08:37:31 UTC (rev 29)
+++ pkg/gt.db/inst/schema/mk_oracle.sql 2010-02-16 19:35:51 UTC (rev 30)
@@ -1,5 +1,6 @@
--
-- Copyright (C) 2009, Perlegen Sciences, Inc.
+-- Copyright (C) 2010, 23andMe, Inc.
--
-- Written by David A. Hinds <dhinds at sonic.net>
--
@@ -30,46 +31,31 @@
created_dt date
);
-create table assay_group
+create table assay_flag
(
- assay_group_id integer primary key,
platform_id integer not null,
- name varchar(64) unique not null,
+ position integer not null,
+ name varchar(64) not null,
description varchar(255),
created_by varchar(64),
created_dt date,
+ constraint af_pk primary key (platform_id, position),
+ constraint af_uniq unique (platform_id, name),
foreign key (platform_id)
references platform(platform_id) on delete cascade
);
--- create table assay_flag
--- (
--- platform_id integer not null,
--- position integer not null,
--- name varchar(64) not null,
--- description varchar(255),
--- created_by varchar(64),
--- created_dt date,
--- constraint af_pk primary key (platform_id, position),
--- constraint af_uniq unique (platform_id, name),
--- foreign key (platform_id)
--- references platform(platform_id) on delete cascade
--- );
-
create table assay
(
assay_id integer primary key,
platform_id integer not null,
- assay_group_id integer not null,
name varchar(255) not null,
- -- flags integer,
+ flags integer,
alleles varchar(255),
probe_seq varchar(255),
constraint assay_uniq unique (platform_id, name),
foreign key (platform_id)
- references platform(platform_id) on delete cascade,
- foreign key (assay_group_id)
- references assay_group(assay_group_id) on delete cascade
+ references platform(platform_id) on delete cascade
);
create table mapping
@@ -350,14 +336,6 @@
into :new.platform_id from dual;
end;
-create sequence assay_group_id_seq;
-create trigger insert_assay_group
-before insert on assay_group for each row
-begin
- select assay_group_id_seq.nextval
- into :new.assay_group_id from dual;
-end;
-
create sequence assay_id_seq;
create trigger insert_assay
before insert on assay for each row
Modified: pkg/gt.db/inst/schema/mk_sqlite.sql
===================================================================
--- pkg/gt.db/inst/schema/mk_sqlite.sql 2010-02-13 08:37:31 UTC (rev 29)
+++ pkg/gt.db/inst/schema/mk_sqlite.sql 2010-02-16 19:35:51 UTC (rev 30)
@@ -1,5 +1,6 @@
--
-- Copyright (C) 2009, Perlegen Sciences, Inc.
+-- Copyright (C) 2010, 23andMe, Inc.
--
-- Written by David A. Hinds <dhinds at sonic.net>
--
@@ -30,46 +31,31 @@
created_dt datetime
);
-create table assay_group
+create table assay_flag
(
- assay_group_id integer primary key,
platform_id integer not null,
- name varchar(64) unique not null,
+ position integer not null,
+ name varchar(64) not null,
description varchar(255),
created_by varchar(64),
created_dt datetime,
+ constraint af_pk primary key (platform_id, position),
+ constraint af_uniq unique (platform_id, name),
foreign key (platform_id)
references platform(platform_id) on delete cascade
);
--- create table assay_flag
--- (
--- platform_id integer not null,
--- position integer not null,
--- name varchar(64) not null,
--- description varchar(255),
--- created_by varchar(64),
--- created_dt datetime,
--- constraint af_pk primary key (platform_id, position),
--- constraint af_uniq unique (platform_id, name),
--- foreign key (platform_id)
--- references platform(platform_id) on delete cascade
--- );
-
create table assay
(
assay_id integer primary key,
platform_id integer not null,
- assay_group_id integer not null,
name varchar(255) not null,
- -- flags integer,
+ flags integer,
alleles varchar(255),
probe_seq varchar(255),
constraint assay_uniq unique (platform_id, name),
foreign key (platform_id)
- references platform(platform_id) on delete cascade,
- foreign key (assay_group_id)
- references assay_group(assay_group_id) on delete cascade
+ references platform(platform_id) on delete cascade
);
create table mapping
Modified: pkg/gt.db/inst/schema/rm_mysql.sql
===================================================================
--- pkg/gt.db/inst/schema/rm_mysql.sql 2010-02-13 08:37:31 UTC (rev 29)
+++ pkg/gt.db/inst/schema/rm_mysql.sql 2010-02-16 19:35:51 UTC (rev 30)
@@ -1,5 +1,6 @@
--
-- Copyright (C) 2009, Perlegen Sciences, Inc.
+-- Copyright (C) 2010, 23andMe, Inc.
--
-- Written by David A. Hinds <dhinds at sonic.net>
--
@@ -34,6 +35,6 @@
drop table project;
drop table assay_position;
drop table mapping;
+drop table assay_flag;
drop table assay;
-drop table assay_group;
drop table platform;
Modified: pkg/gt.db/inst/schema/rm_oracle.sql
===================================================================
--- pkg/gt.db/inst/schema/rm_oracle.sql 2010-02-13 08:37:31 UTC (rev 29)
+++ pkg/gt.db/inst/schema/rm_oracle.sql 2010-02-16 19:35:51 UTC (rev 30)
@@ -1,3 +1,23 @@
+--
+-- Copyright (C) 2009, Perlegen Sciences, Inc.
+-- Copyright (C) 2010, 23andMe, Inc.
+--
+-- Written by David A. Hinds <dhinds at sonic.net>
+--
+-- This is free software; you can redistribute it and/or modify it
+-- under the terms of the GNU General Public License as published by
+-- the Free Software Foundation; either version 3 of the license, or
+-- (at your option) any later version.
+--
+-- This program is distributed in the hope that it will be useful,
+-- but WITHOUT ANY WARRANTY; without even the implied warranty of
+-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+-- GNU General Public License for more details.
+--
+-- You should have received a copy of the GNU General Public License
+-- along with this program. If not, see <http://www.gnu.org/licenses/>
+--
+
drop trigger insert_prcomp;
drop sequence prcomp_id_seq;
drop trigger insert_test;
@@ -20,8 +40,6 @@
drop sequence mapping_id_seq;
drop trigger insert_assay;
drop sequence assay_id_seq;
-drop trigger insert_assay_group;
-drop sequence assay_group_id_seq;
drop trigger insert_platform;
drop sequence platform_id_seq;
drop table prcomp_loading;
@@ -42,6 +60,6 @@
drop table assay_position;
drop table assay_position_flag;
drop table mapping;
+drop table assay_flag;
drop table assay;
-drop table assay_group;
drop table platform;
Modified: pkg/gt.db/inst/schema/rm_sqlite.sql
===================================================================
--- pkg/gt.db/inst/schema/rm_sqlite.sql 2010-02-13 08:37:31 UTC (rev 29)
+++ pkg/gt.db/inst/schema/rm_sqlite.sql 2010-02-16 19:35:51 UTC (rev 30)
@@ -1,5 +1,6 @@
--
-- Copyright (C) 2009, Perlegen Sciences, Inc.
+-- Copyright (C) 2010, 23andMe, Inc.
--
-- Written by David A. Hinds <dhinds at sonic.net>
--
@@ -34,6 +35,6 @@
drop table project;
drop table assay_position;
drop table mapping;
+drop table assay_flag
drop table assay;
-drop table assay_group;
drop table platform;
Modified: pkg/gt.db/man/ls.assay.Rd
===================================================================
--- pkg/gt.db/man/ls.assay.Rd 2010-02-13 08:37:31 UTC (rev 29)
+++ pkg/gt.db/man/ls.assay.Rd 2010-02-16 19:35:51 UTC (rev 30)
@@ -1,5 +1,6 @@
%
% Copyright (C) 2009, Perlegen Sciences, Inc.
+% Copyright (C) 2010, 23andMe, Inc.
%
% Written by David A. Hinds <dhinds at sonic.net>
%
@@ -23,30 +24,25 @@
List definitions of assays associated with a genotyping platform.
}
\usage{
-ls.assay(platform.name, assay.group='\%', show.ids=FALSE)
+ls.assay(platform.name, show.ids=FALSE)
}
\arguments{
\item{platform.name}{a genotyping platform name.}
- \item{assay.group}{an SQL \code{LIKE} expression for matching assay
- group names.}
\item{show.ids}{logical: indicates whether to include values of
database keys.}
}
\value{
- A data frame with one row per assay, and 4 or 6 columns:
- \item{assay.group.id}{if \code{show.ids} is set: a unique integer key
- for the assay group associated with this assay.}
- \item{assay.group}{the assay group associated with this assay.}
+ A data frame with one row per assay, and 4 or 5 columns:
\item{assay.id}{if \code{show.ids} is set: the unique integer ID for
this assay.}
\item{assay.name}{the assay name.}
+ \item{flags}{an integer value composed of single-bit flags.}
\item{alleles}{a slash separated list of allele sequences.}
\item{probe.seq}{the genomic flanking sequence for the assay, with
the variant position denoted by an underscore (\code{'_'}).}
}
\seealso{
- \code{\link{ls.assay.group}}, \code{\link{ls.assay.position}},
- \code{\link{mk.assay}}.
+ \code{\link{ls.assay.position}}, \code{\link{mk.assay}}.
}
\examples{
gt.demo.check()
Deleted: pkg/gt.db/man/ls.assay.group.Rd
===================================================================
--- pkg/gt.db/man/ls.assay.group.Rd 2010-02-13 08:37:31 UTC (rev 29)
+++ pkg/gt.db/man/ls.assay.group.Rd 2010-02-16 19:35:51 UTC (rev 30)
@@ -1,51 +0,0 @@
-%
-% Copyright (C) 2009, Perlegen Sciences, Inc.
-%
-% Written by David A. Hinds <dhinds at sonic.net>
-%
-% This is free software; you can redistribute it and/or modify it
-% under the terms of the GNU General Public License as published by
-% the Free Software Foundation; either version 3 of the license, or
-% (at your option) any later version.
-%
-% This program is distributed in the hope that it will be useful,
-% but WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-% GNU General Public License for more details.
-%
-% You should have received a copy of the GNU General Public License
-% along with this program. If not, see <http://www.gnu.org/licenses/>
-%
-\name{ls.assay.group}
-\alias{ls.assay.group}
-\title{List Assay Groups}
-\description{
- This returns a list of assay groups for the specified genotyping
- platform.
-}
-\usage{
-ls.assay.group(platform.name, show.ids=FALSE)
-}
-\arguments{
- \item{platform.name}{a genotyping platform name.}
- \item{show.ids}{logical: indicates whether to include values of
- database keys.}
-}
-\value{
- A data frame with one row per assay group, and 4 or 5 columns:
- \item{assay.group.id}{if \code{show.ids} is set: a unique integer key
- for this assay group.}
- \item{assay.group}{a short, unique identifier for the assay group.}
- \item{description}{a free-text description of the assay group.}
- \item{created.by}{the user name that created the assay group.}
- \item{created.dt}{the creation date of the assay group.}
-}
-\seealso{
- \code{\link{mk.assay.group}}.
-}
-\examples{
-gt.demo.check()
-ls.assay.group('Demo_Set_1')
-ls.assay.group('Demo_Set_1', show.ids=TRUE)
-}
-\keyword{database}
Modified: pkg/gt.db/man/ls.platform.Rd
===================================================================
--- pkg/gt.db/man/ls.platform.Rd 2010-02-13 08:37:31 UTC (rev 29)
+++ pkg/gt.db/man/ls.platform.Rd 2010-02-16 19:35:51 UTC (rev 30)
@@ -1,5 +1,6 @@
%
% Copyright (C) 2009, Perlegen Sciences, Inc.
+% Copyright (C) 2010, 23andMe, Inc.
%
% Written by David A. Hinds <dhinds at sonic.net>
%
@@ -33,12 +34,11 @@
database keys.}
}
\value{
- A data frame with one row per platform, and 6 or 7 columns:
+ A data frame with one row per platform, and 5 or 6 columns:
\item{platform.id}{if \code{show.ids} is set: a unique integer key
for this platform.}
\item{platform.name}{a short, unique identifier for the platform.}
\item{description}{a free-text description of the platform.}
- \item{assay.groups}{the number of assay groups for this platform.}
\item{datasets}{a count of the number of datasets using this platform.}
\item{created.by}{the user name that created the platform.}
\item{created.dt}{the creation date of the platform.}
Modified: pkg/gt.db/man/mk.assay.Rd
===================================================================
--- pkg/gt.db/man/mk.assay.Rd 2010-02-13 08:37:31 UTC (rev 29)
+++ pkg/gt.db/man/mk.assay.Rd 2010-02-16 19:35:51 UTC (rev 30)
@@ -34,11 +34,10 @@
the data is loaded.}
}
\details{
- A data frame of assay information should provide four columns:
+ A data frame of assay information can provide up to four columns:
\describe{
- \item{assay.group}{an assay group defined with
- \code{\link{mk.assay.group}}.}
\item{assay.name}{a unique name (within this platform) for the assay.}
+ \item{flags}{an optional integer value composed of single-bit flags.}
\item{alleles}{a slash separated list of valid alleles.}
\item{probe.seq}{the genomic flanking sequence for the assay, with
the variant position denoted by an underscore (\code{'_'}).}
Deleted: pkg/gt.db/man/mk.assay.group.Rd
===================================================================
--- pkg/gt.db/man/mk.assay.group.Rd 2010-02-13 08:37:31 UTC (rev 29)
+++ pkg/gt.db/man/mk.assay.group.Rd 2010-02-16 19:35:51 UTC (rev 30)
@@ -1,58 +0,0 @@
-%
-% Copyright (C) 2009, Perlegen Sciences, Inc.
-%
-% Written by David A. Hinds <dhinds at sonic.net>
-%
-% This is free software; you can redistribute it and/or modify it
-% under the terms of the GNU General Public License as published by
-% the Free Software Foundation; either version 3 of the license, or
-% (at your option) any later version.
-%
-% This program is distributed in the hope that it will be useful,
-% but WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-% GNU General Public License for more details.
-%
-% You should have received a copy of the GNU General Public License
-% along with this program. If not, see <http://www.gnu.org/licenses/>
-%
-\name{mk.assay.group}
-\alias{mk.assay.group}
-\alias{rm.assay.group}
-\title{Create or Remove a Genotype Assay Group}
-\description{
- These functions insert or remove entries from the genotyping
- assay group table.
-}
-\usage{
-mk.assay.group(platform.name, assay.group, description)
-rm.assay.group(platform.name, assay.group)
-}
-\arguments{
- \item{platform.name}{the unique platform identifier.}
- \item{assay.group}{an identifier for the assay group.}
- \item{description}{a free-text description of the assay group.}
-}
-\details{
- An assay group and its constituent assays can only be removed if it
- is not in use. Any mappings or datasets that refer to these assays
- must be explicitly deleted first.
-}
-\value{
- If successful, the number of rows inserted in or removed from the
- assay group table (i.e., typically, 1).
-}
-\seealso{
- \code{\link{ls.assay.group}},
- \code{\link{ls.platform}},
- \code{\link{mk.platform}},
- \code{\link{mk.assay}}.
-}
-\examples{\dontrun{
-mk.platform('My_600K', 'My 600K Array Set')
-mk.assay.group('My_600K', 'Des01', '300K Array 1 of 2')
-mk.assay.group('My_600K', 'Des02', '300K Array 2 of 2')
-rm.assay.group('My_600K', c('Des01','Des02'))
-rm.platform('My_600K')
-}}
-\keyword{database}
Modified: pkg/gt.db/man/mk.platform.Rd
===================================================================
--- pkg/gt.db/man/mk.platform.Rd 2010-02-13 08:37:31 UTC (rev 29)
+++ pkg/gt.db/man/mk.platform.Rd 2010-02-16 19:35:51 UTC (rev 30)
@@ -1,5 +1,6 @@
%
% Copyright (C) 2009, Perlegen Sciences, Inc.
+% Copyright (C) 2010, 23andMe, Inc.
%
% Written by David A. Hinds <dhinds at sonic.net>
%
@@ -37,7 +38,7 @@
platform table (i.e., 1).
}
\seealso{
- \code{\link{ls.platform}}, \code{\link{mk.assay.group}}.
+ \code{\link{ls.platform}}.
}
\examples{\dontrun{
mk.platform('GT_800K', 'My 800K Genotyping Platform')
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