Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@44514 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 05/02/2010 03:49:42
Showing 4 changed files

... ...
@@ -377,7 +377,8 @@ in the one function to reduce memory usage (not exported as yet)
377 377
 to save memory.  Instead, 'zero', which indicates which SNPs have zero beads 
378 378
 is stored in the assayData slot.
379 379
  * now store 'zero' with copy number AB intensities in preprocessInfinium2()
380
+ * deleted man pages crlmm.Rd and readIdatFiles.Rd added back
380 381
 
381 382
 2010-02-05 M. Ritchie - committed version 1.5.24
382 383
  * preprocessed allele A and B intensities from copy number and regular SNPs are now saved separately by crlmmIllumina().  The 'intensityFile' argument has been replaced by 'snpFile' and 'cnFile'.
383
- * updated man page for crlmmIllumina()
384 384
\ No newline at end of file
385
+ * updated the following man pages to reflect the above changes and added in current references:  crlmmIllumina.Rd, crlmm.Rd and readIdatFiles.Rd
... ...
@@ -55,8 +55,9 @@ crlmm(filenames, row.names=TRUE, col.names=TRUE,
55 55
   array data. Biostatistics. 2007 Apr;8(2):485-99. Epub 2006 Dec
56 56
   22. PMID: 17189563.
57 57
 
58
-  Carvalho B, Louis TA, Irizarry RA. Describing Uncertainty in
59
-  Genome-wide Genotype Calling. (in prep)
58
+  Carvalho BS, Louis TA, Irizarry RA. 
59
+  Quantifying uncertainty in genotype calls.
60
+  Bioinformatics. 2010 Jan 15;26(2):242-9.
60 61
 }
61 62
 \examples{
62 63
 ## this can be slow
... ...
@@ -7,7 +7,7 @@
7 7
 }
8 8
 \usage{
9 9
 
10
-crlmmIllumina(RG, XY, stripNorm=TRUE, method="quantile",
10
+crlmmIllumina(RG, XY, stripNorm=TRUE, 
11 11
       useTarget=TRUE, row.names=TRUE, col.names=TRUE,
12 12
       probs=c(1/3, 1/3, 1/3), DF=6, SNRMin=5,
13 13
       gender=NULL, seed=1, save.it=FALSE, load.it=FALSE,
... ...
@@ -20,8 +20,7 @@ crlmmIllumina(RG, XY, stripNorm=TRUE, method="quantile",
20 20
   \item{RG}{\code{NChannelSet} containing R and G bead intensities}
21 21
   \item{XY}{\code{NChannelSet} containing X and Y bead intensities}
22 22
   \item{stripNorm}{'logical'.  Should the data be strip-level normalized?}
23
-  \item{method}{'chracter' specifying which normalization method to use.}
24
-  \item{useTarget}{'logical' (only used when \code{stripNorm=TRUE} and \code{method="quantile"}).
23
+  \item{useTarget}{'logical' (only used when \code{stripNorm=TRUE}).
25 24
     Should the reference HapMap intensities be used in strip-level normalization?}
26 25
   \item{row.names}{'logical'. Use rownames - SNP names?}
27 26
   \item{col.names}{'logical'. Use colnames - Sample names?}
... ...
@@ -73,13 +72,18 @@ crlmmIllumina(RG, XY, stripNorm=TRUE, method="quantile",
73 72
 }
74 73
 
75 74
 \references{
75
+  Ritchie ME, Carvalho BS, Hetrick KN, Tavar\'{e} S, Irizarry RA.
76
+  R/Bioconductor software for Illumina's Infinium whole-genome 
77
+  genotyping BeadChips. Bioinformatics. 2009 Oct 1;25(19):2621-3.
78
+
76 79
   Carvalho B, Bengtsson H, Speed TP, Irizarry RA. Exploration,
77 80
   normalization, and genotype calls of high-density oligonucleotide SNP
78 81
   array data. Biostatistics. 2007 Apr;8(2):485-99. Epub 2006 Dec
79 82
   22. PMID: 17189563.
80 83
 
81
-  Carvalho B, Louis TA, Irizarry RA. Describing Uncertainty in
82
-  Genome-wide Genotype Calling. (in prep)
84
+  Carvalho BS, Louis TA, Irizarry RA. 
85
+  Quantifying uncertainty in genotype calls.
86
+  Bioinformatics. 2010 Jan 15;26(2):242-9.
83 87
 }
84 88
 
85 89
 \author{Matt Ritchie}
... ...
@@ -62,6 +62,12 @@ Thanks to Keith Baggerly who provided the code to read in the binary .idat files
62 62
   for SNPs with 0 beads (\code{zero}) for each bead type.
63 63
 }
64 64
 
65
+\references{
66
+  Ritchie ME, Carvalho BS, Hetrick KN, Tavar\'{e} S, Irizarry RA.
67
+  R/Bioconductor software for Illumina's Infinium whole-genome 
68
+  genotyping BeadChips. Bioinformatics. 2009 Oct 1;25(19):2621-3.
69
+}
70
+
65 71
 \author{Matt Ritchie}
66 72
 
67 73
 \examples{