[Gtdb-commits] r25 - in pkg/gt.db: R demo inst/doc inst/schema man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Fri Oct 30 20:49:03 CET 2009 

Author: dahinds
Date: 2009-10-30 20:49:03 +0100 (Fri, 30 Oct 2009)
New Revision: 25

Modified:
   pkg/gt.db/R/admin.R
   pkg/gt.db/R/cluster.R
   pkg/gt.db/R/genotype.R
   pkg/gt.db/demo/setup.gt.demo.R
   pkg/gt.db/inst/doc/gt.db.pdf
   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/man/adjust.gt.calls.Rd
   pkg/gt.db/man/fetch.gt.data.Rd
   pkg/gt.db/man/gt.cluster.plot.Rd
   pkg/gt.db/man/ls.dataset.Rd
   pkg/gt.db/man/mk.assay.data.Rd
   pkg/gt.db/man/mk.dataset.Rd
   pkg/gt.db/man/reshape.gt.data.Rd
Log:
Crude support for handling multiple types of raw supporting data
for genotypes (either signal intensities, or fwd/rev read counts)


Modified: pkg/gt.db/R/admin.R
===================================================================
--- pkg/gt.db/R/admin.R	2009-10-30 19:43:05 UTC (rev 24)
+++ pkg/gt.db/R/admin.R	2009-10-30 19:49:03 UTC (rev 25)
@@ -97,7 +97,8 @@
      "select dataset_id, d.name dataset_name,
              d.project_id, p.name project_name,
              d.platform_id, m.name platform_name,
-             d.description, d.is_hidden, d.created_by, d.created_dt
+             d.description, d.raw_layout, d.is_hidden,
+             d.created_by, d.created_dt
       from dataset d, project p, platform m
       where d.project_id=p.project_id
         and d.platform_id=m.platform_id
@@ -112,16 +113,18 @@
 
 mk.dataset <-
 function(dataset.name, project.name, platform.name,
-         description, is.hidden=FALSE)
+         description, raw.layout=c(NA,'signal','seqread'),
+         is.hidden=FALSE)
 {
+    raw.layout <- match.arg(raw.layout)
     .check.name(dataset.name)
     proj.id <- lookup.id('project', project.name)
     plat.id <- lookup.id('platform', platform.name)
     sql <-
      "insert into dataset
-      values (null, :1, :2, :3, :4, :5, :user:, :sysdate:)"
+      values (null, :1, :2, :3, :4, :5, :6, :user:, :sysdate:)"
     sql.exec(gt.db::.gt.db, sql, proj.id, plat.id, dataset.name,
-             description, is.hidden)
+             description, raw.layout, is.hidden)
 }
 
 rm.dataset <- function(dataset.name)

Modified: pkg/gt.db/R/cluster.R
===================================================================
--- pkg/gt.db/R/cluster.R	2009-10-30 19:43:05 UTC (rev 24)
+++ pkg/gt.db/R/cluster.R	2009-10-30 19:49:03 UTC (rev 25)
@@ -44,7 +44,8 @@
         col=c('#377db8','#e31a1c','#2daf4a','black')
     ),
     superpose.line=list(
-        lty=c(1,1,1,0)
+        lty=c(1,1,1,0),
+        col=c('#377db8','#e31a1c','#2daf4a','black')
     )
 )
 
@@ -59,14 +60,21 @@
         p$xlim <- c(min(p$xlim,p$ylim), max(p$xlim,p$ylim))
         p
     }
-    x <- data$intensity.a
-    y <- data$intensity.b
+    if ('signal.a' %in% names(data)) {
+        x <- data$signal.a
+        y <- data$signal.b
+    } else if ('fwd.a' %in% names(data)) {
+        x <- data$fwd.a+data$rev.a
+        y <- data$fwd.b+data$rev.b
+    } else {
+        stop("raw data not available")
+    }
     n <- factor(data$assay.name)
     if (rescale) {
-      q <- tapply(c(x,y), rep(n,2), range, na.rm=TRUE)
-      q <- do.call('rbind', q)
-      x <- 0.01 + 0.98*(x - q[n,1])/(q[n,2]-q[n,1])
-      y <- 0.01 + 0.98*(y - q[n,1])/(q[n,2]-q[n,1])
+        q <- tapply(c(x,y), rep(n,2), range, na.rm=TRUE)
+        q <- do.call('rbind', q)
+        x <- 0.01 + 0.98*(x - q[n,1])/(q[n,2]-q[n,1])
+        y <- 0.01 + 0.98*(y - q[n,1])/(q[n,2]-q[n,1])
     }
     gt <- data$genotype
     if (is.numeric(gt)) {

Modified: pkg/gt.db/R/genotype.R
===================================================================
--- pkg/gt.db/R/genotype.R	2009-10-30 19:43:05 UTC (rev 24)
+++ pkg/gt.db/R/genotype.R	2009-10-30 19:49:03 UTC (rev 25)
@@ -63,8 +63,8 @@
         and mapping_id=:2')
 
     dset.id <- lookup.id('dataset', dataset.name)
-    platform.name <- ls.dataset(,dataset.name)$platform.name
-    map.id <- lookup.mapping.id(platform.name, mapping.name)
+    ds <- ls.dataset(,dataset.name)
+    map.id <- lookup.mapping.id(ds$platform.name, mapping.name)
     dat <- .sql.prep.data(dset.id, map.id)
     if (!missing(assay.name)) {
         sql <- paste(sql, 'and a.name=:3')
@@ -101,7 +101,7 @@
 
     s <- subset(ls.sample(dataset.name), !is.na(position))
     s <- s[order(s$position),]
-    if (!all.equal(s$position,1:nrow(s)) ||
+    if (!identical(s$position,1:nrow(s)) ||
         any(nchar(d$genotype) != nrow(s))) {
         stop('inconsistent sample layout information!');
     }
@@ -111,7 +111,8 @@
                      show.ids, 'assay.data.id')
     class(d) <- c('gt.data','data.frame')
     keep.attr(d, dataset.name=dataset.name,
-              platform.name=platform.name,
+              raw.layout=ds$raw.layout,
+              platform.name=ds$platform.name,
               mapping.name=names(map.id),
               gender=g, sample.name=s$sample.name)
 }
@@ -210,15 +211,28 @@
     if (!is.null(gt.data$qscore)) {
         d$qscore <- as.integer(cvt.fn(gt.data$qscore))
     }
-    if (!is.null(gt.data$raw.data)) {
-        n <- nrow(d)
+    if (is.null(gt.data$raw.data))
+        return(d)
+    f <- attr(gt.data,'raw.layout')
+    if (is.null(f))
+        stop('raw data layout unavailable')
+    nr <- nrow(d)
+    if (f == 'signal') {
         i <- readBin(cvt.fn(gt.data$raw.data), what='int',
-                     n=2*n, size=2, signed=FALSE, endian='little')
+                     n=2*nr, size=2, signed=FALSE, endian='little')
         i <- na.if(i, 65535)
-        dim(i) <- c(2,n)
-        d <- cbind(d, intensity.a=i[1,], intensity.b=i[2,])
+        dim(i) <- c(2,nr)
+        cbind(d, signal.a=i[1,], signal.b=i[2,])
+    } else if (f == 'seqread') {
+        i <- readBin(cvt.fn(gt.data$raw.data), what='int',
+                     n=4*nr, size=1, signed=FALSE, endian='little')
+        i <- na.if(i, 255)
+        dim(i) <- c(4,nr)
+        cbind(d, fwd.a=i[1,], rev.a=i[2,], fwd.b=i[3,], rev.b=i[4,])
+    } else {
+        warning('unknown raw data layout')
+        d
     }
-    d
 }
 
 .mask.dat <- function(str, mask, squeeze=FALSE)

Modified: pkg/gt.db/demo/setup.gt.demo.R
===================================================================
--- pkg/gt.db/demo/setup.gt.demo.R	2009-10-30 19:43:05 UTC (rev 24)
+++ pkg/gt.db/demo/setup.gt.demo.R	2009-10-30 19:49:03 UTC (rev 25)
@@ -54,7 +54,8 @@
 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', 'Demo (HapMap) Dataset #2')
+mk.dataset('Demo_2', 'Demo', 'Demo_Set_2',
+           'Demo (HapMap) Dataset #2', 'signal')
 mk.flag('assay_data', 'Demo_2', 1, 'pass', 'Passed QC filters')
 
 # now load the data: note that there are some duplicate samples

Modified: pkg/gt.db/inst/doc/gt.db.pdf
===================================================================
--- pkg/gt.db/inst/doc/gt.db.pdf	2009-10-30 19:43:05 UTC (rev 24)
+++ pkg/gt.db/inst/doc/gt.db.pdf	2009-10-30 19:49:03 UTC (rev 25)
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-îMÀö,ý®Ê¢uãSÃòLš¦ T½†Ñh¸®f/mˆ¾Vi|Óĝ@™V%ä{Ù½ÑÖLÈË8]U³Mjûœ8ÄS)2™Ù–iÃ\µA«¯Þ Jk40 ê´}¤4sØ GÀ|‘^–výadu¨æ­ÈÕÅaTfV&ÄE³ß癵6³E(gé¡pÂB±ÇC0º\Œ	ˆpìvóÕÉ*ìÆ>Ã2üß"qu&¾§›öyk3µIS.ĦÉ/F®lŠ•Mz¨¦±t\
-^˃clùíD°Ã,xˆÉV9Ç“³‚ÁØ5¨Ë\TgføáÕ[d—ÿ¼}¤Â•
-‰G‡´+‹æìÔúýÞ}L%¢Šƒ_U´á2Ýá­|5í#è$žŽº À”Ž¢îæ+ö9o.cú–	š ‘–õრÿ¬¤^ԍîêáÂGKí ›–Úá“Õ#¡vØÛA
-QÇ:zñù³ÀHÁöê»EÝx L×Jø—T½™Ùv¸ñ¸òB½©$	¦m£í‰U»åLª¹BK úñ‡V¦_T¦´†¼ºÕ««&Ë×z©Ut¸SjŽbxÒå¾ßßâKÈMÙú±Ï‹½rÄ1|Üý¼4Ǧ
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/gtdb -r 25

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