[Qpcr-commits] r136 - pkg/ReadqPCR/man

[noreply at r-forge.r-project.org]

Author: jperkins
Date: 2011-05-25 13:37:32 +0200 (Wed, 25 May 2011)
New Revision: 136

Modified:
   pkg/ReadqPCR/man/read.qPCR.Rd
   pkg/ReadqPCR/man/read.taqman.Rd
Log:
ReadqPCR man pages finished

Modified: pkg/ReadqPCR/man/read.qPCR.Rd
===================================================================
--- pkg/ReadqPCR/man/read.qPCR.Rd	2011-05-21 17:03:22 UTC (rev 135)
+++ pkg/ReadqPCR/man/read.qPCR.Rd	2011-05-25 11:37:32 UTC (rev 136)
@@ -2,10 +2,10 @@
 \alias{read.qPCR}
 \alias{read_qPCRBatch}
 \alias{checkValidqPCRFilename}
-\title{ Read Taqman qPCR data into ExpressionSet }
+\title{ Read user formatted qPCR data and produce a qPCRBatch }
 \description{
-  Reads RT-qPCR data in format specified in the ReadqPCR vignette to object of class
-  \code{"ExpressionSet"}.
+  Reads RT-qPCR data in format specified in the ReadqPCR vignette and uses the data to populate an object of class
+  \code{"qPCRBatch"}.
 }
 \usage{
 read.qPCR(filename = character(0),
@@ -14,11 +14,11 @@
           verbose = FALSE)
 }
 \arguments{
-  \item{filename}{file name in a character vector.}
+  \item{filename}{file name (must be formatted as shown in vignette).}
   \item{phenoData}{an \code{\link[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}}
      object, a \code{character} of length one, or a \code{data.frame}.}
   \item{notes}{notes.}
-  \item{verbose}{verbosity flag.}
+  \item{verbose}{verbosity flag. If true more messages are given to the user on the processing steps}
 }
 \details{
   Permits the user to read in qPCR Ct value data in a predefined format 
@@ -26,7 +26,7 @@
   phenotypic data and further notes about the data. If \code{phenoData} is a \code{data.frame}, 
   it is converted to an \code{AnnotatedDataFrame}. If it is \code{NULL} then a default object
   of class \code{AnnotatedDataFrame} is created, whose \code{pData} is a
-  \code{data.frame} with rownames being the names of the CEL files, and
+  \code{data.frame} with rownames being the names of the samples, and
   with one column \code{sample} with an integer index. 
   More details on how technical replicates are handled in the \code{ReadqPCR} package vignette
 }

Modified: pkg/ReadqPCR/man/read.taqman.Rd
===================================================================
--- pkg/ReadqPCR/man/read.taqman.Rd	2011-05-21 17:03:22 UTC (rev 135)
+++ pkg/ReadqPCR/man/read.taqman.Rd	2011-05-25 11:37:32 UTC (rev 136)
@@ -2,10 +2,10 @@
 \alias{read.taqman}
 \alias{read_TaqBatch}
 \alias{checkValidTaqmanFilenames}
-\title{ Read Taqman qPCR data into ExpressionSet }
+\title{ Read Taqman qPCR data and produce a qPCRBatch }
 \description{
-  Reads Taqman RT-qPCR data to object of class
-  \code{"ExpressionSet"}.
+  Reads Taqman RT-qPCR data and uses the data to populate an object of class
+  \code{"qPCRBatch"}.
 }
 \usage{
 read.taqman(\dots,
@@ -21,7 +21,7 @@
   \code{\link[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}}
   object, a \code{character} of length one, or a \code{data.frame}.}
   \item{notes}{notes.}
-  \item{verbose}{verbosity flag.}
+  \item{verbose}{verbosity flag. If true more messages are given to the user on the processing steps}
 }
 \details{
   Permits the user to read in qPCR Ct value data from an sds output file, 
@@ -29,7 +29,7 @@
   is a \code{data.frame}, it is converted to an \code{AnnotatedDataFrame}. If it
   is \code{NULL} then a default object  of class \code{AnnotatedDataFrame} is
   created, whose \code{pData} is a \code{data.frame} with rownames being the
-  names of the CEL files, and with one column \code{sample} with an integer index.
+  names of the , and with one column \code{sample} with an integer index.
   More details on how technical replicates are handled in the \code{ReadqPCR}
 package vignette
 }