git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58616 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 01/10/2011 04:44:58
| ... | ... |
@@ -7,7 +7,7 @@ |
| 7 | 7 |
} |
| 8 | 8 |
\usage{
|
| 9 | 9 |
|
| 10 |
-crlmmIllumina(RG, XY, stripNorm=TRUE, |
|
| 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, mixtureSampleSize=10^5, |
| ... | ... |
@@ -64,7 +64,7 @@ crlmmIllumina(RG, XY, stripNorm=TRUE, |
| 64 | 64 |
|
| 65 | 65 |
\references{
|
| 66 | 66 |
Ritchie ME, Carvalho BS, Hetrick KN, Tavar\'{e} S, Irizarry RA.
|
| 67 |
- R/Bioconductor software for Illumina's Infinium whole-genome |
|
| 67 |
+ R/Bioconductor software for Illumina's Infinium whole-genome |
|
| 68 | 68 |
genotyping BeadChips. Bioinformatics. 2009 Oct 1;25(19):2621-3. |
| 69 | 69 |
|
| 70 | 70 |
Carvalho B, Bengtsson H, Speed TP, Irizarry RA. Exploration, |
| ... | ... |
@@ -72,7 +72,7 @@ crlmmIllumina(RG, XY, stripNorm=TRUE, |
| 72 | 72 |
array data. Biostatistics. 2007 Apr;8(2):485-99. Epub 2006 Dec |
| 73 | 73 |
22. PMID: 17189563. |
| 74 | 74 |
|
| 75 |
- Carvalho BS, Louis TA, Irizarry RA. |
|
| 75 |
+ Carvalho BS, Louis TA, Irizarry RA. |
|
| 76 | 76 |
Quantifying uncertainty in genotype calls. |
| 77 | 77 |
Bioinformatics. 2010 Jan 15;26(2):242-9. |
| 78 | 78 |
} |
| ... | ... |
@@ -10,10 +10,10 @@ |
| 10 | 10 |
crlmmIlluminaV2(sampleSheet=NULL, arrayNames=NULL, ids=NULL, path=".", |
| 11 | 11 |
arrayInfoColNames=list(barcode="SentrixBarcode_A", position="SentrixPosition_A"), |
| 12 | 12 |
highDensity=FALSE, sep="_", fileExt=list(green="Grn.idat", red="Red.idat"), |
| 13 |
- saveDate=FALSE, stripNorm=TRUE, useTarget=TRUE, |
|
| 14 |
- row.names=TRUE, col.names=TRUE, probs=c(1/3, 1/3, 1/3), |
|
| 15 |
- DF=6, SNRMin=5, gender=NULL, seed=1, mixtureSampleSize=10^5, |
|
| 16 |
- eps=0.1, verbose=TRUE, cdfName, sns, recallMin=10, |
|
| 13 |
+ saveDate=FALSE, stripNorm=TRUE, useTarget=TRUE, |
|
| 14 |
+ row.names=TRUE, col.names=TRUE, probs=c(1/3, 1/3, 1/3), |
|
| 15 |
+ DF=6, SNRMin=5, gender=NULL, seed=1, mixtureSampleSize=10^5, |
|
| 16 |
+ eps=0.1, verbose=TRUE, cdfName, sns, recallMin=10, |
|
| 17 | 17 |
recallRegMin=1000, returnParams=FALSE, badSNP=.7) |
| 18 | 18 |
} |
| 19 | 19 |
|
| ... | ... |
@@ -83,13 +83,13 @@ crlmmIlluminaV2(sampleSheet=NULL, arrayNames=NULL, ids=NULL, path=".", |
| 83 | 83 |
} |
| 84 | 84 |
|
| 85 | 85 |
\details{
|
| 86 |
- This function combines the reading of data from idat files using |
|
| 87 |
- \code{readIdatFiles} and genotyping to reduce memory usage.
|
|
| 86 |
+ This function combines the reading of data from idat files using |
|
| 87 |
+ \code{readIdatFiles} and genotyping to reduce memory usage.
|
|
| 88 | 88 |
} |
| 89 | 89 |
|
| 90 | 90 |
\references{
|
| 91 | 91 |
Ritchie ME, Carvalho BS, Hetrick KN, Tavar\'{e} S, Irizarry RA.
|
| 92 |
- R/Bioconductor software for Illumina's Infinium whole-genome |
|
| 92 |
+ R/Bioconductor software for Illumina's Infinium whole-genome |
|
| 93 | 93 |
genotyping BeadChips. Bioinformatics. 2009 Oct 1;25(19):2621-3. |
| 94 | 94 |
|
| 95 | 95 |
Carvalho B, Bengtsson H, Speed TP, Irizarry RA. Exploration, |
| ... | ... |
@@ -97,7 +97,7 @@ crlmmIlluminaV2(sampleSheet=NULL, arrayNames=NULL, ids=NULL, path=".", |
| 97 | 97 |
array data. Biostatistics. 2007 Apr;8(2):485-99. Epub 2006 Dec |
| 98 | 98 |
22. PMID: 17189563. |
| 99 | 99 |
|
| 100 |
- Carvalho BS, Louis TA, Irizarry RA. |
|
| 100 |
+ Carvalho BS, Louis TA, Irizarry RA. |
|
| 101 | 101 |
Quantifying uncertainty in genotype calls. |
| 102 | 102 |
Bioinformatics. 2010 Jan 15;26(2):242-9. |
| 103 | 103 |
} |