#### Added nopackage option for krlmm

unknown authored on 03/05/2016 23:39:54
Showing1 changed files
 ... ... @@ -16,9 +16,9 @@ 16 16  } 17 17  \usage{ 18 18  genotypeInf(cnSet, mixtureParams, probs = rep(1/3, 3), SNRMin = 5, 19 -recallMin = 10, recallRegMin = 1000, verbose = TRUE, returnParams = 20 -TRUE, badSNP = 0.7, gender = NULL, DF = 6, cdfName, call.method="crlmm",  21 -trueCalls = NULL) 19 + recallMin = 10, recallRegMin = 1000, verbose = TRUE, returnParams = TRUE,  20 + badSNP = 0.7, gender = NULL, DF = 6, cdfName, nopackage.norm="quantile", 21 + call.method="crlmm", trueCalls = NULL) 22 22  } 23 23  %- maybe also 'usage' for other objects documented here. 24 24  \arguments{ ... ... @@ -44,6 +44,8 @@ trueCalls = NULL) 44 44  t-distribution.} 45 45  \item{cdfName}{\code{character} string indicating which annotation 46 46  package to load.} 47 + \item{nopackage.norm}{character string specifying normalization to be used when \code{cdfName}='nopackage'. 48 + Options are 'none', 'quantile' (within channel, between array) and 'quantileloess'.} 47 49  \item{call.method}{character string specifying the genotype calling algorithm to use ('crlmm' or 'krlmm').} 48 50  \item{trueCalls}{ matrix specifying known Genotype calls for a subset of samples and features(1 - AA, 2 - AB, 3 - BB).} 49 51  }

#### fix conflict in description

Rob Scharp authored on 30/09/2013 14:07:17
Showing1 changed files
 ... ... @@ -17,7 +17,8 @@ 17 17  \usage{ 18 18  genotypeInf(cnSet, mixtureParams, probs = rep(1/3, 3), SNRMin = 5, 19 19  recallMin = 10, recallRegMin = 1000, verbose = TRUE, returnParams = 20 -TRUE, badSNP = 0.7, gender = NULL, DF = 6, cdfName, call.method="crlmm") 20 +TRUE, badSNP = 0.7, gender = NULL, DF = 6, cdfName, call.method="crlmm",  21 +trueCalls = NULL) 21 22  } 22 23  %- maybe also 'usage' for other objects documented here. 23 24  \arguments{ ... ... @@ -44,6 +45,7 @@ TRUE, badSNP = 0.7, gender = NULL, DF = 6, cdfName, call.method="crlmm") 44 45  \item{cdfName}{\code{character} string indicating which annotation 45 46  package to load.} 46 47  \item{call.method}{character string specifying the genotype calling algorithm to use ('crlmm' or 'krlmm').} 48 + \item{trueCalls}{ matrix specifying known Genotype calls for a subset of samples and features(1 - AA, 2 - AB, 3 - BB).} 47 49  } 48 50   49 51  \details{ ... ... @@ -60,6 +62,16 @@ TRUE, badSNP = 0.7, gender = NULL, DF = 6, cdfName, call.method="crlmm") 60 62  the transformation 'round(-1000*log2(1-p))', where p is the 61 63  probability. The function \code{i2P} can be used to convert the 62 64  integers back to the scale of probabilities. 65 + 66 + An optional \code{trueCalls} argument can be provided to KRLMM method 67 + which contains known genotype calls(can contain some NAs) for some  68 + samples and SNPs. This will used to compute KRLMM parameters by calling 69 + \code{vglm} function from \code{VGAM} package. 70 + 71 + The KRLMM method makes use of functions provided in \code{parallel}  72 + package to speed up the process. It by default initialises up to  73 + 8 clusters. This is configurable by setting up an option named  74 + "krlmm.cores", e.g. options("krlmm.cores" = 16).  63 75  } 64 76   65 77  \value{

#### merging from collab

* collab:
Added Human Omni Express Exome 8 v1.1b as a supported chip
updated version number of pacakge and man pages to reflect these changes
skeleton for krlmm capability added. genotype.Illumina() can now take and XY object as input
update copynumber.Rnw to use BafLrrSetList
update namespace

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

Rob Scharp authored on 31/07/2013 01:37:34
Showing1 changed files
 ... ... @@ -9,7 +9,7 @@ 9 9  \description{ 10 10   11 11  Genotyping of Illumina Infinium II arrays. This function 12 - provides CRLMM genotypes and confidence scores for the the 12 + provides CRLMM/KRLMM genotypes and confidence scores for the the 13 13  polymorphic markers and is a required step prior to copy 14 14  number estimation. 15 15   ... ... @@ -17,7 +17,7 @@ 17 17  \usage{ 18 18  genotypeInf(cnSet, mixtureParams, probs = rep(1/3, 3), SNRMin = 5, 19 19  recallMin = 10, recallRegMin = 1000, verbose = TRUE, returnParams = 20 -TRUE, badSNP = 0.7, gender = NULL, DF = 6, cdfName) 20 +TRUE, badSNP = 0.7, gender = NULL, DF = 6, cdfName, call.method="crlmm") 21 21  } 22 22  %- maybe also 'usage' for other objects documented here. 23 23  \arguments{ ... ... @@ -43,11 +43,12 @@ TRUE, badSNP = 0.7, gender = NULL, DF = 6, cdfName) 43 43  t-distribution.} 44 44  \item{cdfName}{\code{character} string indicating which annotation 45 45  package to load.} 46 + \item{call.method}{character string specifying the genotype calling algorithm to use ('crlmm' or 'krlmm').} 46 47  } 47 48   48 49  \details{ 49 50   50 - The CRLMM genotype calls and confidence scores are written to 51 + The genotype calls and confidence scores are written to 51 52  file using \code{ff} protocols for I/O. For the most part, 52 53  the calls and confidence scores can be accessed as though the 53 54  data is in memory through the methods \code{snpCall} and

#### Merge branch 'mymac'

* mymac:
update vignettes in inst/scripts
Change argument of validCEL to celfiles
Update constructInf to accommodate GenomeDataFrame class for featureData
bump version to 1.13.7
Streamlne some of the Rd files
getFeatureData returns GenomeAnnotatedDataFrame
Remove imports from methods. Remove pdf of illumina_copynumber.pdf (large file) and copynumber.pdf
getFeatureDAta returns GenomeAnnotatedDataFrame
Remove separate vignette for copy number in inst/scripts. Include copynumber section in both affy and illumina pipelines.
update documentation files for genotype.Illumina, preprocessInf, and genotypeInf (cdfName added as argument. Indicate that 'batch' should be a character string)
pass cdfName to genotypeInf and preprocessInf
add unitTests and cn-functions for 'simple usage'
Combine AffyPreprocess and copynumber. Combine IlluminaPreprocess and copynumber
remove depency on ff to allow installation on my mac

Rob Scharp authored on 17/01/2012 19:13:44
Showing1 changed files
 ... ... @@ -15,7 +15,9 @@ 15 15   16 16  } 17 17  \usage{ 18 -genotypeInf(cnSet, mixtureParams, probs = rep(1/3, 3), SNRMin = 5, recallMin = 10, recallRegMin = 1000, verbose = TRUE, returnParams = TRUE, badSNP = 0.7, gender = NULL, DF = 6) 18 +genotypeInf(cnSet, mixtureParams, probs = rep(1/3, 3), SNRMin = 5, 19 +recallMin = 10, recallRegMin = 1000, verbose = TRUE, returnParams = 20 +TRUE, badSNP = 0.7, gender = NULL, DF = 6, cdfName) 19 21  } 20 22  %- maybe also 'usage' for other objects documented here. 21 23  \arguments{ ... ... @@ -37,7 +39,10 @@ genotypeInf(cnSet, mixtureParams, probs = rep(1/3, 3), SNRMin = 5, recallMin = 1 37 39  \item{gender}{ integer vector ( male = 1, female =2 ) or missing, 38 40  with same length as filenames. If missing, the gender is 39 41  predicted.} 40 - \item{DF}{'integer' with number of degrees of freedom to use with t-distribution.} 42 + \item{DF}{'integer' with number of degrees of freedom to use with 43 + t-distribution.} 44 + \item{cdfName}{\code{character} string indicating which annotation 45 + package to load.} 41 46  } 42 47   43 48  \details{ ... ... @@ -69,7 +74,8 @@ confidence scores can be retrieved using accessors for the 69 74  R. Scharpf 70 75  } 71 76  \seealso{ 72 - \code{\link{crlmm}}, \code{\link{snpCall}}, \code{\link{snpCallProbability}} 77 + \code{\link{crlmm}}, \code{\link{snpCall}}, 78 + \code{\link{snpCallProbability}}, \code{\link{annotationPackages}} 73 79  } 74 80  \examples{ 75 81  ## See the 'illumina_copynumber' vignette in inst/scripts of

#### Rewrote illumina_copynumber vignette. Add functions and docmentation for constructInf, preprocessInf, and genotypeInf.

Rob Scharp authored on 30/03/2011 02:40:07
Showing1 changed files
 1 1 new file mode 100644 ... ... @@ -0,0 +1,78 @@ 1 +\name{genotypeInf} 2 +\alias{genotypeInf} 3 + 4 +\title{ 5 + 6 + Genotyping of Illumina Infinium II arrays. 7 + 8 +} 9 +\description{ 10 + 11 + Genotyping of Illumina Infinium II arrays. This function 12 + provides CRLMM genotypes and confidence scores for the the 13 + polymorphic markers and is a required step prior to copy 14 + number estimation. 15 + 16 +} 17 +\usage{ 18 +genotypeInf(cnSet, mixtureParams, probs = rep(1/3, 3), SNRMin = 5, recallMin = 10, recallRegMin = 1000, verbose = TRUE, returnParams = TRUE, badSNP = 0.7, gender = NULL, DF = 6) 19 +} 20 +%- maybe also 'usage' for other objects documented here. 21 +\arguments{ 22 + \item{cnSet}{An object of class \code{CNSet}} 23 + \item{mixtureParams}{ 24 + \code{data.frame} containing mixture model parameters needed for 25 + genotyping. The mixture model parameters are estimated from the 26 + \code{preprocessInf} function. 27 + } 28 + \item{probs}{'numeric' vector with priors for AA, AB and BB.} 29 + \item{SNRMin}{'numeric' scalar defining the minimum SNR used to filter 30 + out samples.} 31 + \item{recallMin}{Minimum number of samples for recalibration. } 32 + \item{recallRegMin}{Minimum number of SNP's for regression.} 33 + \item{verbose}{ 'logical.' Whether to print descriptive messages during processing.} 34 + \item{returnParams}{'logical'. Return recalibrated parameters from crlmm.} 35 + \item{badSNP}{'numeric'. Threshold to flag as bad SNP (affects 36 + batchQC)} 37 + \item{gender}{ integer vector ( male = 1, female =2 ) or missing, 38 + with same length as filenames. If missing, the gender is 39 + predicted.} 40 + \item{DF}{'integer' with number of degrees of freedom to use with t-distribution.} 41 +} 42 + 43 +\details{ 44 + 45 + The CRLMM genotype calls and confidence scores are written to 46 + file using \code{ff} protocols for I/O. For the most part, 47 + the calls and confidence scores can be accessed as though the 48 + data is in memory through the methods \code{snpCall} and 49 + \code{snpCallProbability}, respectively. 50 + 51 + The genotype calls are stored using an integer representation: 1 52 + - AA, 2 - AB, 3 - BB. Similarly, the call probabilities are 53 + stored using an integer representation to reduce file size using 54 + the transformation 'round(-1000*log2(1-p))', where p is the 55 + probability. The function \code{i2P} can be used to convert the 56 + integers back to the scale of probabilities. 57 + } 58 + 59 +\value{ 60 + 61 +Logical. If the genotyping is completed, the value 'TRUE' is 62 +returned. Note that \code{assayData} elements 'call' and 63 +'callProbability' are updated on disk. Therefore, the genotypes and 64 +confidence scores can be retrieved using accessors for the 65 +\code{CNSet} class. 66 + 67 +} 68 +\author{ 69 +R. Scharpf 70 +} 71 +\seealso{ 72 + \code{\link{crlmm}}, \code{\link{snpCall}}, \code{\link{snpCallProbability}} 73 +} 74 +\examples{ 75 + ## See the 'illumina_copynumber' vignette in inst/scripts of 76 + ## the source package 77 +} 78 +\keyword{classif} 0 79 \ No newline at end of file