1. crlmm
  2. man
  3. snprma.Rd
Browse code

Fixes in docs and code reorganization

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45608 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 31/03/2010 11:16:26
Showing 1 changed files
man/snprma.Rd
History View file @ 9ac2da3
... ... 
@@ -56,8 +56,8 @@ snprma2(filenames, mixtureSampleSize = 10^5, fitMixture = FALSE, eps = 0.1, verb
56 56 
   the use of clusters or multiple cores (via snow package) to speed up preprocessing.
57 57 
   }
58 58 
 \examples{
59 
-if (require(genomewidesnp5Crlmm) & require(hapmapsnp5) & require(oligoClasses)){
60 
-  path <- system.file("celFiles", package="hapmapsnp5")
59 
+if (require(genomewidesnp6Crlmm) & require(hapmapsnp6) & require(oligoClasses)){
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+  path <- system.file("celFiles", package="hapmapsnp6")
61 61
62 62 
   ## the filenames with full path...
63 63 
   ## very useful when genotyping samples not in the working directory
... ... 
@@ -76,7 +76,7 @@ ocProbesets(50000)
76 76 
 ## setup cluster - 8 cores on the machine
77 77 
 setCluster(8, "SOCK")
78 78
79 
-path <- system.file("celFiles", package="hapmapsnp5")
79 
+path <- system.file("celFiles", package="hapmapsnp6")
80 80 
 cels <- list.celfiles(path, full.names=TRUE)
81 81 
 snprmaOutput <- snprma2(cels)
82 82
Browse code

HPC for snprma/crlmm on Affy

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45498 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 25/03/2010 13:14:54
Showing 1 changed files
man/snprma.Rd
History View file @ f0da692
... ... 
@@ -1,6 +1,7 @@
1 1 
 \name{snprma}
2 2 
 \Rdversion{1.1}
3 3 
 \alias{snprma}
4 
+\alias{snprma2}
4 5
5 6 
 \title{
6 7 
   Preprocessing tool for SNP arrays.
... ... 
@@ -12,6 +13,7 @@
12 13 
 }
13 14 
 \usage{
14 15 
 snprma(filenames, mixtureSampleSize = 10^5, fitMixture = FALSE, eps = 0.1, verbose = TRUE, seed = 1, cdfName, sns)
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+snprma2(filenames, mixtureSampleSize = 10^5, fitMixture = FALSE, eps = 0.1, verbose = TRUE, seed = 1, cdfName, sns)
15 17 
 }
16 18 
 \arguments{
17 19 
   \item{filenames}{
... ... 
@@ -49,6 +51,10 @@ snprma(filenames, mixtureSampleSize = 10^5, fitMixture = FALSE, eps = 0.1, verbo
49 51 
   \item{mixtureParams}{Parameters from mixture model}
50 52 
   \item{cdfName}{Name of the CDF}
51 53 
 }
54 
+\details{
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+  'snprma2' allows one to genotype very large datasets (via ff package) and also permits
56 
+  the use of clusters or multiple cores (via snow package) to speed up preprocessing.
57 
+  }
52 58 
 \examples{
53 59 
 if (require(genomewidesnp5Crlmm) & require(hapmapsnp5) & require(oligoClasses)){
54 60 
   path <- system.file("celFiles", package="hapmapsnp5")
... ... 
@@ -60,6 +66,22 @@ if (require(genomewidesnp5Crlmm) & require(hapmapsnp5) & require(oligoClasses)){
60 66 
   snprmaOutput[["A"]][1:10,]
61 67 
   snprmaOutput[["B"]][1:10,]
62 68 
 }
69 
+\dontrun{
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+## HPC Example
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+library(ff)
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+library(snow)
73 
+library(crlmm)
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+## genotype 50K SNPs at a time
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+ocProbesets(50000)
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+## setup cluster - 8 cores on the machine
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+setCluster(8, "SOCK")
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+
79 
+path <- system.file("celFiles", package="hapmapsnp5")
80 
+cels <- list.celfiles(path, full.names=TRUE)
81 
+snprmaOutput <- snprma2(cels)
82 
+
83 
+}
84 
+
63 85 
 }
64 86 
 \keyword{manip}
65 87 
 \keyword{classif}
Browse code

roll back to crlmm version 1.5.24

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45126 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 10/03/2010 01:27:04
Showing 1 changed files
man/snprma.Rd
History View file @ 5fcfed7
... ... 
@@ -6,15 +6,12 @@
6 6 
   Preprocessing tool for SNP arrays.
7 7 
 }
8 8 
 \description{
9 
-
10 9 
   SNPRMA will preprocess SNP chips. The preprocessing consists of
11 10 
   quantile normalization to a known target distribution and
12 
-  summarization to the SNP-Allele level. This function is not
13 
-  typically called directly.
14 
-
11 
+  summarization to the SNP-Allele level.
15 12 
 }
16 13 
 \usage{
17 
-snprma(filenames, mixtureSampleSize = 10^5, fitMixture = FALSE, eps = 0.1, verbose = TRUE, seed = 1, cdfName, AFile="A.rda", BFile="B.rda")
14 
+snprma(filenames, mixtureSampleSize = 10^5, fitMixture = FALSE, eps = 0.1, verbose = TRUE, seed = 1, cdfName, sns)
18 15 
 }
19 16 
 \arguments{
20 17 
   \item{filenames}{
... ... 
@@ -36,18 +33,11 @@ snprma(filenames, mixtureSampleSize = 10^5, fitMixture = FALSE, eps = 0.1, verbo
36 33 
     Seed to be used when sampling.
37 34 
 }
38 35 
   \item{cdfName}{
39 
-    cdfName: 'genomewidesnp5', 'genomewidesnp6'
40 
-    See \code{validCdfNames}.
36 
+    cdfName: 'GenomeWideSnp\_5', 'GenomeWideSnp\_6'
37 
+}
38 
+  \item{sns}{
39 
+    Sample names.
41 40 
 }
42 
-
43 
-\item{AFile}{'character' for naming the quantile normalized
44 
-intensities for the A allele.  This object also contains the
45 
-normalized intensities for the nonpolymorphic loci, depending on the
46 
-platform }
47 
-
48 
-\item{BFile}{'character' for naming the quantile normalized
49 
-intensities for the B allele.  }
50 
-
51 41 
 }
52 42 
 \value{
53 43 
   \item{A}{Summarized intensities for Allele A}
... ... 
@@ -66,11 +56,9 @@ if (require(genomewidesnp5Crlmm) & require(hapmapsnp5) & require(oligoClasses)){
66 56 
   ## the filenames with full path...
67 57 
   ## very useful when genotyping samples not in the working directory
68 58 
   cels <- list.celfiles(path, full.names=TRUE)
69 
-  snprmaResult <-  snprma(cels, cdfName="genomewidesnp5")
70 
-  str(snprmaResult)
71 
-  load("A.rda")
72 
-  A[1:10, ]
73 
-  unlink(list("A.rda", "B.rda"))
59 
+  snprmaOutput <- snprma(cels)
60 
+  snprmaOutput[["A"]][1:10,]
61 
+  snprmaOutput[["B"]][1:10,]
74 62 
 }
75 63 
 }
76 64 
 \keyword{manip}
Browse code

several updates for ff. new classes for affy/illumina processing. More s4-style code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45083 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 08/03/2010 04:46:55
Showing 1 changed files
man/snprma.Rd
History View file @ a13f66d
... ... 
@@ -14,7 +14,7 @@
14 14
15 15 
 }
16 16 
 \usage{
17 
-snprma(filenames, mixtureSampleSize = 10^5, fitMixture = FALSE, eps = 0.1, verbose = TRUE, seed = 1, cdfName, sns, AFile="A.rda", BFile="B.rda")
17 
+snprma(filenames, mixtureSampleSize = 10^5, fitMixture = FALSE, eps = 0.1, verbose = TRUE, seed = 1, cdfName, AFile="A.rda", BFile="B.rda")
18 18 
 }
19 19 
 \arguments{
20 20 
   \item{filenames}{
... ... 
@@ -40,10 +40,6 @@ snprma(filenames, mixtureSampleSize = 10^5, fitMixture = FALSE, eps = 0.1, verbo
40 40 
     See \code{validCdfNames}.
41 41 
 }
42 42
43 
-  \item{sns}{
44 
-    Sample names.
45 
-}
46 
-
47 43 
 \item{AFile}{'character' for naming the quantile normalized
48 44 
 intensities for the A allele.  This object also contains the
49 45 
 normalized intensities for the nonpolymorphic loci, depending on the
... ... 
@@ -70,9 +66,11 @@ if (require(genomewidesnp5Crlmm) & require(hapmapsnp5) & require(oligoClasses)){
70 66 
   ## the filenames with full path...
71 67 
   ## very useful when genotyping samples not in the working directory
72 68 
   cels <- list.celfiles(path, full.names=TRUE)
73 
-  snprmaOutput <- snprma(cels)
74 
-  snprmaOutput[["A"]][1:10,]
75 
-  snprmaOutput[["B"]][1:10,]
69 
+  snprmaResult <-  snprma(cels, cdfName="genomewidesnp5")
70 
+  str(snprmaResult)
71 
+  load("A.rda")
72 
+  A[1:10, ]
73 
+  unlink(list("A.rda", "B.rda"))
76 74 
 }
77 75 
 }
78 76 
 \keyword{manip}
Browse code

begin adding support for ff. added an option to use poe

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@44778 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 20/02/2010 23:39:45
Showing 1 changed files
man/snprma.Rd
History View file @ 7e1d14d
... ... 
@@ -6,12 +6,15 @@
6 6 
   Preprocessing tool for SNP arrays.
7 7 
 }
8 8 
 \description{
9 
+
9 10 
   SNPRMA will preprocess SNP chips. The preprocessing consists of
10 11 
   quantile normalization to a known target distribution and
11 
-  summarization to the SNP-Allele level.
12 
+  summarization to the SNP-Allele level. This function is not
13 
+  typically called directly.
14 
+
12 15 
 }
13 16 
 \usage{
14 
-snprma(filenames, mixtureSampleSize = 10^5, fitMixture = FALSE, eps = 0.1, verbose = TRUE, seed = 1, cdfName, sns)
17 
+snprma(filenames, mixtureSampleSize = 10^5, fitMixture = FALSE, eps = 0.1, verbose = TRUE, seed = 1, cdfName, sns, AFile="A.rda", BFile="B.rda")
15 18 
 }
16 19 
 \arguments{
17 20 
   \item{filenames}{
... ... 
@@ -33,11 +36,22 @@ snprma(filenames, mixtureSampleSize = 10^5, fitMixture = FALSE, eps = 0.1, verbo
33 36 
     Seed to be used when sampling.
34 37 
 }
35 38 
   \item{cdfName}{
36 
-    cdfName: 'GenomeWideSnp\_5', 'GenomeWideSnp\_6'
39 
+    cdfName: 'genomewidesnp5', 'genomewidesnp6'
40 
+    See \code{validCdfNames}.
37 41 
 }
42 
+
38 43 
   \item{sns}{
39 44 
     Sample names.
40 45 
 }
46 
+
47 
+\item{AFile}{'character' for naming the quantile normalized
48 
+intensities for the A allele.  This object also contains the
49 
+normalized intensities for the nonpolymorphic loci, depending on the
50 
+platform }
51 
+
52 
+\item{BFile}{'character' for naming the quantile normalized
53 
+intensities for the B allele.  }
54 
+
41 55 
 }
42 56 
 \value{
43 57 
   \item{A}{Summarized intensities for Allele A}
Browse code

updated first half of inst/scripts/copynumber.Rnw, as well as a few of the help files

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@43728 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 23/12/2009 10:57:10
Showing 1 changed files
man/snprma.Rd
History View file @ 7ae22f5
... ... 
@@ -50,7 +50,7 @@ snprma(filenames, mixtureSampleSize = 10^5, fitMixture = FALSE, eps = 0.1, verbo
50 50 
   \item{cdfName}{Name of the CDF}
51 51 
 }
52 52 
 \examples{
53 
-if (require(genomewidesnp5Crlmm) & require(hapmapsnp5)){
53 
+if (require(genomewidesnp5Crlmm) & require(hapmapsnp5) & require(oligoClasses)){
54 54 
   path <- system.file("celFiles", package="hapmapsnp5")
55 55
56 56 
   ## the filenames with full path...
Browse code

added classes/methods for intermediate files and copy number analysis; added wrapper for preprocessing and genotypes.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@40309 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 25/06/2009 12:54:08
Showing 1 changed files
man/snprma.Rd
History View file @ 38fb1b8
... ... 
@@ -33,7 +33,7 @@ snprma(filenames, mixtureSampleSize = 10^5, fitMixture = FALSE, eps = 0.1, verbo
33 33 
     Seed to be used when sampling.
34 34 
 }
35 35 
   \item{cdfName}{
36 
-    cdfName: 'GenomeWideSnp_5', 'GenomeWideSnp_6'
36 
+    cdfName: 'GenomeWideSnp\_5', 'GenomeWideSnp\_6'
37 37 
 }
38 38 
   \item{sns}{
39 39 
     Sample names.
Browse code

Added documentation for SNPRMA

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38548 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 07/04/2009 11:22:53
Showing 1 changed files
man/snprma.Rd
History View file @ 268a6dc
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,65 @@
1 
+\name{snprma}
2 
+\Rdversion{1.1}
3 
+\alias{snprma}
4 
+
5 
+\title{
6 
+  Preprocessing tool for SNP arrays.
7 
+}
8 
+\description{
9 
+  SNPRMA will preprocess SNP chips. The preprocessing consists of
10 
+  quantile normalization to a known target distribution and
11 
+  summarization to the SNP-Allele level.
12 
+}
13 
+\usage{
14 
+snprma(filenames, mixtureSampleSize = 10^5, fitMixture = FALSE, eps = 0.1, verbose = TRUE, seed = 1, cdfName, sns)
15 
+}
16 
+\arguments{
17 
+  \item{filenames}{
18 
+    'character' vector with file names.
19 
+}
20 
+  \item{mixtureSampleSize}{
21 
+    Sample size to be use when fitting the mixture model.
22 
+}
23 
+  \item{fitMixture}{
24 
+    'logical'. Fit the mixture model?
25 
+}
26 
+  \item{eps}{
27 
+    Stop criteria.
28 
+}
29 
+  \item{verbose}{
30 
+    'logical'.
31 
+}
32 
+  \item{seed}{
33 
+    Seed to be used when sampling.
34 
+}
35 
+  \item{cdfName}{
36 
+    cdfName: 'GenomeWideSnp_5', 'GenomeWideSnp_6'
37 
+}
38 
+  \item{sns}{
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+    Sample names.
40 
+}
41 
+}
42 
+\value{
43 
+  \item{A}{Summarized intensities for Allele A}
44 
+  \item{B}{Summarized intensities for Allele B}
45 
+  \item{sns}{Sample names}
46 
+  \item{gns}{SNP names}
47 
+  \item{SNR}{Signal-to-noise ratio}
48 
+  \item{SKW}{Skewness}
49 
+  \item{mixtureParams}{Parameters from mixture model}
50 
+  \item{cdfName}{Name of the CDF}
51 
+}
52 
+\examples{
53 
+if (require(genomewidesnp5Crlmm) & require(hapmapsnp5)){
54 
+  path <- system.file("celFiles", package="hapmapsnp5")
55 
+
56 
+  ## the filenames with full path...
57 
+  ## very useful when genotyping samples not in the working directory
58 
+  cels <- list.celfiles(path, full.names=TRUE)
59 
+  snprmaOutput <- snprma(cels)
60 
+  snprmaOutput[["A"]][1:10,]
61 
+  snprmaOutput[["B"]][1:10,]
62 
+}
63 
+}
64 
+\keyword{manip}
65 
+\keyword{classif}