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 The 'intensityFile' argument has been replaced by 'snpFile' and 'cnFile'.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