From 50dbbdb8ab269a026e9a0bdd9bf951d01fc9d47e Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 16 Nov 2010 22:46:07 +0000
Subject: [PATCH] Retrieves per-sample or per-lane metrics from the SQUID
 database and populates a dataframe with the results.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4693 348d0f76-0448-11de-a6fe-93d51630548a
---
 R/src/gsalib/R/read.squidmetrics.R    | 22 ++++++++++++
 R/src/gsalib/man/read.squidmetrics.Rd | 48 +++++++++++++++++++++++++++
 2 files changed, 70 insertions(+)
 create mode 100644 R/src/gsalib/R/read.squidmetrics.R
 create mode 100644 R/src/gsalib/man/read.squidmetrics.Rd

diff --git a/R/src/gsalib/R/read.squidmetrics.R b/R/src/gsalib/R/read.squidmetrics.R
new file mode 100644
index 000000000..24e1cc658
--- /dev/null
+++ b/R/src/gsalib/R/read.squidmetrics.R
@@ -0,0 +1,22 @@
+read.squidmetrics = function(project, bylane = FALSE) {
+    suppressMessages(library(ROracle));
+
+    drv = dbDriver("Oracle");
+    con = dbConnect(drv, "REPORTING/REPORTING@ora01:1521/SEQPROD");
+
+    if (bylane) {
+        rs  = dbSendQuery(con, statement = paste("SELECT * FROM ILLUMINA_PICARD_METRICS"));
+        d = fetch(rs, n=-1);
+        dbHasCompleted(rs);
+        dbClearResult(rs);
+    } else {
+        rs = dbSendQuery(con, statement = paste("SELECT * FROM ILLUMINA_SAMPLE_STATUS_AGG"));
+        d = fetch(rs, n=-1);
+        dbHasCompleted(rs);
+        dbClearResult(rs);
+    }
+
+    oraCloseDriver(drv);
+
+    d;
+}
diff --git a/R/src/gsalib/man/read.squidmetrics.Rd b/R/src/gsalib/man/read.squidmetrics.Rd
new file mode 100644
index 000000000..223f9b450
--- /dev/null
+++ b/R/src/gsalib/man/read.squidmetrics.Rd
@@ -0,0 +1,48 @@
+\name{read.squidmetrics}
+\alias{read.squidmetrics}
+\title{
+read.squidmetrics
+}
+\description{
+Reads metrics for a specified SQUID project into a dataframe.
+}
+\usage{
+read.squidmetrics("C315")
+}
+\arguments{
+  \item{project}{
+The project for which metrics should be obtained.
+}
+  \item{bylane}{
+If TRUE, obtains per-lane metrics rather than the default per-sample metrics.
+}
+}
+\details{
+%%  ~~ If necessary, more details than the description above ~~
+}
+\value{
+%%  ~Describe the value returned
+%%  If it is a LIST, use
+%%  \item{comp1 }{Description of 'comp1'}
+%%  \item{comp2 }{Description of 'comp2'}
+%% ...
+Returns a data frame with samples (or lanes) as the row and the metric as the column.
+}
+\references{
+%% ~put references to the literature/web site here ~
+}
+\author{
+Kiran Garimella
+}
+\note{
+This method will only work within the Broad Institute internal network.
+}
+
+\seealso{
+%% ~~objects to See Also as \code{\link{help}}, ~~~
+}
+\examples{
+## Obtain metrics for project C315.
+d = read.squidmetrics("C315");
+}
+\keyword{ ~kwd1 }