1. basecallQC
  2. R
  3. allMethods.R
Browse code

Fixes and updates

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/basecallQC@130196 bc3139a8-67e5-0310-9ffc-ced21a209358

Tom Carroll authored on 08/06/2017 16:16:28
Showing 1 changed files
R/allMethods.R
History View file @ 5e9aab2
... ... 
@@ -1,68 +1,72 @@
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-#' Read lengths
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-#'
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-#' Read lengths as defined by runParameters.xml
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-#'
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-#' @usage
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-#' \S4method{readlengths}{BCL2FastQparams}(object)
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-#'
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-#' @docType methods
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-#' @name readlengths
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-#' @rdname readlengths
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-#' @aliases readlengths readlengths,BCL2FastQparams-method, readlengths.bcl2fastqparams
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-#'
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-#' @author Thomas Carroll
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-#' @examples
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-#' fileLocations <- system.file("extdata",package="basecallQC")
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-#' runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE)
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-#' config <- dir(fileLocations,pattern="config.ini",full.names=TRUE)
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-#' bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),verbose=FALSE)
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-#' readlength <- readlengths(bcl2fastqparams)
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-#' @param object A BCL2FastQparams object
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-#' @return Read lengths as defined runParamaeters.xml
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-#' @export
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-readlengths.bcl2fastqparams <-  function (object)
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-{
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-  dplyr::select(object@RunParameters$runParams,Read1,Read2) %>% mutate_all(as.numeric)
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-}
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-
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-setGeneric("readlengths", function(object="BCL2FastQparams") standardGeneric("readlengths"))
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-
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-#' @rdname readlengths
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-#' @export
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-setMethod("readlengths", signature(object="BCL2FastQparams"), readlengths.bcl2fastqparams)
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-
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-#' Index lengths
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-#'
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-#' Index lengths as defined by runParameters.xml
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-#'
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-#' @usage
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-#' \S4method{indexlengths}{BCL2FastQparams}(object)
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-#'
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-#' @docType methods
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-#' @name indexlengths
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-#' @rdname indexlengths
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-#' @aliases indexlengths indexlengths,BCL2FastQparams-method, indexlengths.bcl2fastqparams
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-#'
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-#' @author Thomas Carroll
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-#' @examples
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-#' fileLocations <- system.file("extdata",package="basecallQC")
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-#' runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE)
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-#' config <- dir(fileLocations,pattern="config.ini",full.names=TRUE)
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-#' bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),verbose=FALSE)
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-#' indexlength <- indexlengths(bcl2fastqparams)
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-#' @param object A BCL2FastQparams object
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-#' @return Index lengths as defined runParameters.xml.
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-#' @export
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-indexlengths.bcl2fastqparams <-  function (object)
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-{
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-  dplyr::select(object@RunParameters$runParams,IndexRead1,IndexRead2)  %>% mutate_all(as.numeric)
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-}
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-
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-setGeneric("indexlengths", function(object="BCL2FastQparams") standardGeneric("indexlengths"))
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-
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-#' @rdname indexlengths
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-#' @export
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-setMethod("indexlengths", signature(object="BCL2FastQparams"), indexlengths.bcl2fastqparams)
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-
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-
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-
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+#' Read lengths
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+#'
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+#' Read lengths as defined by runParameters.xml
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+#'
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+#' @usage
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+#' \S4method{readlengths}{BCL2FastQparams}(object)
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+#'
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+#' @docType methods
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+#' @name readlengths
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+#' @rdname readlengths
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+#' @aliases readlengths readlengths,BCL2FastQparams-method, readlengths.bcl2fastqparams
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+#'
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+#' @author Thomas Carroll
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+#' @examples
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+#' fileLocations <- system.file("extdata",package="basecallQC")
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+#' runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE)
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+#' config <- dir(fileLocations,pattern="config.ini",full.names=TRUE)
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+#' bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),verbose=FALSE)
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+#' readlength <- readlengths(bcl2fastqparams)
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+#' @param object A BCL2FastQparams object
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+#' @return Read lengths as defined runParamaeters.xml
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+#' @export
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+readlengths.bcl2fastqparams <-  function (object)
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+{
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+  dplyr::select(object@RunParameters$runParams,Read1,Read2) %>% mutate_all(as.numeric)
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+}
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+
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+setGeneric("readlengths", function(object="BCL2FastQparams") standardGeneric("readlengths"))
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+
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+#' @rdname readlengths
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+#' @export
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+setMethod("readlengths", signature(object="BCL2FastQparams"), readlengths.bcl2fastqparams)
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+
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+#' Index lengths
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+#'
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+#' Index lengths as defined by runParameters.xml
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+#'
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+#' @usage
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+#' \S4method{indexlengths}{BCL2FastQparams}(object)
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+#'
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+#' @docType methods
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+#' @name indexlengths
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+#' @rdname indexlengths
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+#' @aliases indexlengths indexlengths,BCL2FastQparams-method, indexlengths.bcl2fastqparams
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+#'
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+#' @author Thomas Carroll
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+#' @examples
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+#' fileLocations <- system.file("extdata",package="basecallQC")
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+#' runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE)
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+#' config <- dir(fileLocations,pattern="config.ini",full.names=TRUE)
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+#' bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),verbose=FALSE)
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+#' indexlength <- indexlengths(bcl2fastqparams)
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+#' @param object A BCL2FastQparams object
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+#' @return Index lengths as defined runParameters.xml.
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+#' @export
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+indexlengths.bcl2fastqparams <-  function (object)
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+{
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+  dplyr::select(object@RunParameters$runParams,IndexRead1,IndexRead2)  %>% mutate_all(as.numeric)
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+}
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+
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+setGeneric("indexlengths", function(object="BCL2FastQparams") standardGeneric("indexlengths"))
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+
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+#' @rdname indexlengths
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+#' @export
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+setMethod("indexlengths", signature(object="BCL2FastQparams"), indexlengths.bcl2fastqparams)
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+
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+
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+readPattern <- function(bcl2fastqparams){
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+  c(readlengths(bcl2fastqparams)[1],indexlengths(bcl2fastqparams)[1],
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+    indexlengths(bcl2fastqparams)[2],readlengths(bcl2fastqparams)[2])
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+}
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+
Browse code

Adding RaggedExperiment, basecallQC, CATALYST, GenomicScores, IMAS, semisup, ImpulseDE2, methylInheritance, biotmle, biotmleData, BLMA, TCGAWorkflow, metavizr

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/basecallQC@128350 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 07/04/2017 20:14:00
Showing 1 changed files
R/allMethods.R
History View file @ 82d9bc8
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,68 @@
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+#' Read lengths
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+#'
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+#' Read lengths as defined by runParameters.xml
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+#'
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+#' @usage
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+#' \S4method{readlengths}{BCL2FastQparams}(object)
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+#'
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+#' @docType methods
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+#' @name readlengths
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+#' @rdname readlengths
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+#' @aliases readlengths readlengths,BCL2FastQparams-method, readlengths.bcl2fastqparams
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+#'
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+#' @author Thomas Carroll
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+#' @examples
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+#' fileLocations <- system.file("extdata",package="basecallQC")
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+#' runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE)
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+#' config <- dir(fileLocations,pattern="config.ini",full.names=TRUE)
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+#' bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),verbose=FALSE)
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+#' readlength <- readlengths(bcl2fastqparams)
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+#' @param object A BCL2FastQparams object
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+#' @return Read lengths as defined runParamaeters.xml
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+#' @export
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+readlengths.bcl2fastqparams <-  function (object)
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+{
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+  dplyr::select(object@RunParameters$runParams,Read1,Read2) %>% mutate_all(as.numeric)
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+}
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+
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+setGeneric("readlengths", function(object="BCL2FastQparams") standardGeneric("readlengths"))
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+
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+#' @rdname readlengths
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+#' @export
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+setMethod("readlengths", signature(object="BCL2FastQparams"), readlengths.bcl2fastqparams)
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+
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+#' Index lengths
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+#'
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+#' Index lengths as defined by runParameters.xml
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+#'
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+#' @usage
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+#' \S4method{indexlengths}{BCL2FastQparams}(object)
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+#'
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+#' @docType methods
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+#' @name indexlengths
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+#' @rdname indexlengths
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+#' @aliases indexlengths indexlengths,BCL2FastQparams-method, indexlengths.bcl2fastqparams
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+#'
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+#' @author Thomas Carroll
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+#' @examples
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+#' fileLocations <- system.file("extdata",package="basecallQC")
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+#' runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE)
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+#' config <- dir(fileLocations,pattern="config.ini",full.names=TRUE)
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+#' bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),verbose=FALSE)
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+#' indexlength <- indexlengths(bcl2fastqparams)
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+#' @param object A BCL2FastQparams object
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+#' @return Index lengths as defined runParameters.xml.
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+#' @export
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+indexlengths.bcl2fastqparams <-  function (object)
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+{
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+  dplyr::select(object@RunParameters$runParams,IndexRead1,IndexRead2)  %>% mutate_all(as.numeric)
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+}
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+
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+setGeneric("indexlengths", function(object="BCL2FastQparams") standardGeneric("indexlengths"))
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+
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+#' @rdname indexlengths
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+#' @export
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+setMethod("indexlengths", signature(object="BCL2FastQparams"), indexlengths.bcl2fastqparams)
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+
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+
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+