Browse code

Add doc for cnSetExample

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@59041 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 11/10/2011 12:18:21
Showing 2 changed files

... ...
@@ -1,7 +1,7 @@
1 1
 Package: crlmm
2 2
 Type: Package
3 3
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4
-Version: 1.11.57
4
+Version: 1.11.58
5 5
 Date: 2010-12-10
6 6
 Author: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry
7 7
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
8 8
new file mode 100644
... ...
@@ -0,0 +1,109 @@
1
+\name{cnSetExample}
2
+\alias{cnSetExample}
3
+\alias{cnSetExample2}
4
+\docType{data}
5
+\title{
6
+	Object of class 'CNSet'
7
+}
8
+\description{
9
+
10
+	The data for the first 16 polymorphic markers in the HapMap analysis.
11
+
12
+}
13
+\details{
14
+  This object was created from the copynumber vignette in inst/scripts.
15
+}
16
+\usage{
17
+
18
+data(cnSetExample)
19
+data(cnSetExample2)
20
+
21
+}
22
+\format{
23
+  The data illustrates the \code{CNSet-class}, with
24
+	\code{assayData} containing the quantile-normalized
25
+	intensities for the A and B alleles, genotype calls and
26
+	confidence scores.  New slots that specific to copy number
27
+	estimation are \code{batch} and \code{batchStatistics}.
28
+
29
+}
30
+\examples{
31
+\dontshow{
32
+\dontrun{
33
+
34
+      ## hapmap phase 3 data
35
+      data(hapmapSet, package="CnvScripts")
36
+      marker.index <- which(chromosome(hapmapSet) == 8)
37
+      marker.index <- marker.index[1:60e3]
38
+      sample.CNSet <- hapmapSet[marker.index, c(1168:1169)]
39
+      cnSetExample <- sample.CNSet
40
+      save(cnSetExample, file="~/Software/crlmm/data/cnSetExample.rda")
41
+      ## 2 samples, many markers
42
+
43
+      ## all samples, a few markers
44
+      snp.index <- which(isSnp(hapmapSet))[1:100]
45
+      np.index <- which(!isSnp(hapmapSet))[1:100]
46
+      marker.index <- c(snp.index, np.index)
47
+      sample.CNSet2 <- hapmapSet[marker.index, ]
48
+      sample.CNSet2$gender <- sample.CNSet2$gender[]
49
+      sample.CNSet2$SKW <- sample.CNSet2$SKW[]
50
+      sample.CNSet2$SNR <- sample.CNSet2$SNR[]
51
+      cnSetExample2 <- sample.CNSet2
52
+      save(cnSetExample2, file="~/Software/crlmm/data/cnSetExample2.rda")
53
+}
54
+}
55
+data(cnSetExample)
56
+## --------------------------------------------------
57
+## accessors for the feature-level info
58
+## --------------------------------------------------
59
+chromosome(cnSetExample)[1:5]
60
+position(cnSetExample)[1:5]
61
+isSnp(cnSetExample)[1:5]
62
+table(isSnp(cnSetExample))
63
+## --------------------------------------------------
64
+## sample-level statistics computed by crlmm
65
+## --------------------------------------------------
66
+varLabels(cnSetExample)
67
+## accessors for sample-level statistics
68
+## The signal to noise ratio (SNR)
69
+cnSetExample$SNR[]
70
+## the skew
71
+cnSetExample$SKW[]
72
+## the gender (gender is imputed unless specified in the call to crlmm)
73
+table(cnSetExample$gender[])  ## 1=male, 2=female
74
+## --------------------------------------------------
75
+## batchStatistics
76
+## -------------------------------------------------- estimate of
77
+## intercept from linear model
78
+dim(nu(cnSetExample, "A"))
79
+## background for the A allele in the 2 batches for the
80
+## first 5 markers
81
+nu(cnSetExample, "A")[1:5, ]
82
+## background for the B allele in the 2 batches for the
83
+## first 5 markers
84
+nu(cnSetExample, "B")[1:5, ]
85
+## the slope
86
+phi(cnSetExample, "A")[1:5, ]
87
+
88
+## --------------------------------------------------
89
+## calculating allele-specific copy number
90
+## --------------------------------------------------
91
+(ca <- CA(cnSetExample, i=1:5, j=1:2))
92
+## copy number for allele B, first 5 markers, first 2 samples
93
+(cb <- CB(cnSetExample, i=1:5, j=1:2))
94
+index <- which(!isSnp(cnSetExample))[1:5]
95
+cn2 <- CA(cnSetExample, i=index, j=1:2)
96
+## note, cb is 0 at nonpolymorphic loci
97
+CB(cnSetExample, i=index, j=1:2)
98
+## A shortcut for total copy number
99
+cn3 <- totalCopynumber(cnSetExample, i=1:5, j=1:2)
100
+all.equal(cn3, ca+cb)
101
+cn4 <- totalCopynumber(cnSetExample, i=index, j=1:2)
102
+all.equal(cn4, cn2)
103
+
104
+## markers 1-5, all samples
105
+cn5 <- totalCopynumber(cnSetExample, i=1:5)
106
+## all markers, samples 1-2
107
+cn6 <- totalCopynumber(cnSetExample, j=1:2)
108
+}
109
+\keyword{datasets}