1. basecallQC
  2. R
  3. reporting.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/reporting.R
History View file @ 5e9aab2
... ... 
@@ -1,50 +1,50 @@
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-#' Generate basecallQC report
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-#'
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-#' Creates a summary report from basecalling and demultiplexing metrics.
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-#'
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-#' @usage
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-#' \S4method{reportBCL}{basecallQC}(object,reportOut,reportOutDir,output,reportRMDfile,FQQC)
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-#' @docType methods
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-#' @name reportBCL
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-#' @rdname reportBCL
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-#' @aliases reportBCL reportBCL,baseCallQC-method
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-#' @author Thomas Carroll
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-#'
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-#' @param object A basecall QC object as returned from basecallQC() function
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-#' @param reportOut Name of report file
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-#' @param reportOutDir Directory for the report file
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-#' @param output Whether the report contains frozen or sortable tables. Options are "static" and "html"
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-#' @param reportRMDfile RMD to be used for reporting. (Default uses standard report template)
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-#' @param FQQC TRUE or FALSE, whether to run ShortRead fastq QC on any fastQ in output directory.
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-#' @return An HTML report is written to file.
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-#' @import stringr XML RColorBrewer methods raster ShortRead prettydoc
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-#' @examples
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-#'
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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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-#' sampleSheet <- dir(fileLocations,pattern="*\\.csv",full.names=TRUE)
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-#' outDir <- file.path(fileLocations,"Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX/")
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-#' bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),outDir,verbose=FALSE)
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-#' bclQC <- basecallQC(bcl2fastqparams,RunMetaData=NULL,sampleSheet)
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-#' reportBCL(bclQC,"TestReport.html",output="html")
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-#' @export
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-reportBCL.basecallQC <- function(object,reportOut="report.html",reportOutDir=getwd(),
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-                      output="static",reportRMDfile=NULL,FQQC=FALSE){
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-  BCLQCreport <- object
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-  doFQQC <- FQQC
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-  fileLocations <- system.file("extdata",package="basecallQC")
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-  if(is.null(reportRMDfile)){
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-    reportRMD <- file.path(fileLocations,"reportRMDs","basecallqcreport.Rmd")
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-  }
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-  if(!file.exists(reportRMD)) stop()
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-  render(reportRMD,
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-         output_file = reportOut,output_dir=reportOutDir,params=list(title=paste0("basecallQC")))
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-}
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-
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-setGeneric("reportBCL", function(object="basecallQC",reportOut="character",reportOutDir="character",
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-                                 output="character",reportRMDfile=NULL,FQQC=FALSE) standardGeneric("reportBCL"))
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-
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-#' @rdname reportBCL
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-#' @export
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-setMethod("reportBCL", signature(object="basecallQC"), reportBCL.basecallQC)
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+#' Generate basecallQC report
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+#'
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+#' Creates a summary report from basecalling and demultiplexing metrics.
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+#'
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+#' @usage
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+#' \S4method{reportBCL}{basecallQC}(object,reportOut,reportOutDir,output,reportRMDfile,FQQC)
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+#' @docType methods
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+#' @name reportBCL
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+#' @rdname reportBCL
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+#' @aliases reportBCL reportBCL,baseCallQC-method
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+#' @author Thomas Carroll
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+#'
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+#' @param object A basecall QC object as returned from basecallQC() function
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+#' @param reportOut Name of report file
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+#' @param reportOutDir Directory for the report file
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+#' @param output Whether the report contains frozen or sortable tables. Options are "static" and "html"
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+#' @param reportRMDfile RMD to be used for reporting. (Default uses standard report template)
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+#' @param FQQC TRUE or FALSE, whether to run ShortRead fastq QC on any fastQ in output directory.
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+#' @return An HTML report is written to file.
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+#' @import stringr XML RColorBrewer methods raster ShortRead prettydoc
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+#' @examples
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+#'
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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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+#' sampleSheet <- dir(fileLocations,pattern="*\\.csv",full.names=TRUE)
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+#' outDir <- file.path(fileLocations,"Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX/")
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+#' bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),outDir,verbose=FALSE)
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+#' bclQC <- basecallQC(bcl2fastqparams,RunMetaData=NULL,sampleSheet)
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+#' reportBCL(bclQC,"TestReport.html",output="html")
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+#' @export
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+reportBCL.basecallQC <- function(object,reportOut="report.html",reportOutDir=getwd(),
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+                      output="static",reportRMDfile=NULL,FQQC=FALSE){
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+  BCLQCreport <- object
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+  doFQQC <- FQQC
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+  fileLocations <- system.file("extdata",package="basecallQC")
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+  if(is.null(reportRMDfile)){
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+    reportRMD <- file.path(fileLocations,"reportRMDs","basecallqcreport.Rmd")
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+  }
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+  if(!file.exists(reportRMD)) stop()
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+  render(reportRMD,
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+         output_file = reportOut,output_dir=reportOutDir,params=list(title=paste0("basecallQC")))
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+}
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+
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+setGeneric("reportBCL", function(object="basecallQC",reportOut="character",reportOutDir="character",
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+                                 output="character",reportRMDfile=NULL,FQQC=FALSE) standardGeneric("reportBCL"))
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+
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+#' @rdname reportBCL
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+#' @export
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+setMethod("reportBCL", signature(object="basecallQC"), reportBCL.basecallQC)
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/reporting.R
History View file @ 82d9bc8
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,50 @@
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+#' Generate basecallQC report
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+#'
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+#' Creates a summary report from basecalling and demultiplexing metrics.
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+#'
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+#' @usage
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+#' \S4method{reportBCL}{basecallQC}(object,reportOut,reportOutDir,output,reportRMDfile,FQQC)
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+#' @docType methods
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+#' @name reportBCL
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+#' @rdname reportBCL
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+#' @aliases reportBCL reportBCL,baseCallQC-method
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+#' @author Thomas Carroll
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+#'
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+#' @param object A basecall QC object as returned from basecallQC() function
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+#' @param reportOut Name of report file
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+#' @param reportOutDir Directory for the report file
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+#' @param output Whether the report contains frozen or sortable tables. Options are "static" and "html"
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+#' @param reportRMDfile RMD to be used for reporting. (Default uses standard report template)
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+#' @param FQQC TRUE or FALSE, whether to run ShortRead fastq QC on any fastQ in output directory.
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+#' @return An HTML report is written to file.
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+#' @import stringr XML RColorBrewer methods raster ShortRead prettydoc
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+#' @examples
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+#'
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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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+#' sampleSheet <- dir(fileLocations,pattern="*\\.csv",full.names=TRUE)
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+#' outDir <- file.path(fileLocations,"Runs/161105_D00467_0205_AC9L0AANXX/C9L0AANXX/")
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+#' bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),outDir,verbose=FALSE)
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+#' bclQC <- basecallQC(bcl2fastqparams,RunMetaData=NULL,sampleSheet)
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+#' reportBCL(bclQC,"TestReport.html",output="html")
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+#' @export
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+reportBCL.basecallQC <- function(object,reportOut="report.html",reportOutDir=getwd(),
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+                      output="static",reportRMDfile=NULL,FQQC=FALSE){
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+  BCLQCreport <- object
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+  doFQQC <- FQQC
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+  fileLocations <- system.file("extdata",package="basecallQC")
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+  if(is.null(reportRMDfile)){
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+    reportRMD <- file.path(fileLocations,"reportRMDs","basecallqcreport.Rmd")
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+  }
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+  if(!file.exists(reportRMD)) stop()
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+  render(reportRMD,
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+         output_file = reportOut,output_dir=reportOutDir,params=list(title=paste0("basecallQC")))
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+}
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+
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+setGeneric("reportBCL", function(object="basecallQC",reportOut="character",reportOutDir="character",
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+                                 output="character",reportRMDfile=NULL,FQQC=FALSE) standardGeneric("reportBCL"))
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+
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+#' @rdname reportBCL
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+#' @export
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+setMethod("reportBCL", signature(object="basecallQC"), reportBCL.basecallQC)