... | ... |
@@ -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 The 'intensityFile' argument has been replaced by 'snpFile' and 'cnFile'.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 |
} |
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\examples{ |
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## 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} |
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\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 |
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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{ |