[Qpcr-commits] r128 - in pkg/NormqPCR: . man

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

Author: stamats
Date: 2011-02-15 18:59:59 +0100 (Tue, 15 Feb 2011)
New Revision: 128

Modified:
   pkg/NormqPCR/NAMESPACE
   pkg/NormqPCR/man/deltaCt.Rd
   pkg/NormqPCR/man/deltaDeltaCt.Rd
Log:
some minor corrections

Modified: pkg/NormqPCR/NAMESPACE
===================================================================
--- pkg/NormqPCR/NAMESPACE	2011-02-15 17:34:49 UTC (rev 127)
+++ pkg/NormqPCR/NAMESPACE	2011-02-15 17:59:59 UTC (rev 128)
@@ -1,2 +1,15 @@
-importClasses(qPCRSet)
-export(geomMean,stabMeasureM,stabMeasureRho,selectHKs,deltaCt,replaceNAs,deltaDeltaCt,makeAllNAs,combineTechReps,replaceAboveCutOff,makeAllNAs,replaceNAs,plotDCt,plotDdCt)
+importClassesFrom(ReadqPCR, qPCRBatch)
+export(geomMean,
+       stabMeasureM,
+       stabMeasureRho,
+       selectHKs,
+       deltaCt,
+       replaceNAs,
+       deltaDeltaCt,
+       makeAllNAs,
+       combineTechReps,
+       replaceAboveCutOff,
+       makeAllNAs,
+       replaceNAs,
+       plotDCt,
+       plotDdCt)

Modified: pkg/NormqPCR/man/deltaCt.Rd
===================================================================
--- pkg/NormqPCR/man/deltaCt.Rd	2011-02-15 17:34:49 UTC (rev 127)
+++ pkg/NormqPCR/man/deltaCt.Rd	2011-02-15 17:59:59 UTC (rev 128)
@@ -6,17 +6,14 @@
 Normalise qPCR eset using a given housekeeping gene as control, then perform differential expression analysis using the delta delta Ct method
 }
 \usage{
-deltaCt(qPCRBatch, hkgs, combineHkgs)
+deltaCt(qPCRBatch, hkgs, combineHkgs=FALSE, calc="arith")
 }
 \arguments{
-  \item{qPCRBatch}{ Expression set containing qPCR data. 
+  \item{qPCRBatch}{ Expression set containing qPCR data. }
+  \item{hkgs}{ String containing the name of the name of the housekeeping gene which will be used to normalise the rest of the genes.}
+  \item{combineHkgs}{  Logical - if TRUE, then as long as more than one housekeeper given for argument hkgs, it will combine the housekeepers by finding the geometric mean. Housekeepers can be found using geNorm or NormFinder algorithms.}
+  \item{calc}{ use arithmetic or geometric mean.}
 }
-  \item{hkgs}{ String containing the name of the name of the housekeeping gene which will be used to normalise the rest of the genes.
-}
-  \item{combineHkgs}{  Logical - if TRUE, then as long as more than one housekeeper given for argument hkgs, it will combine the housekeepers by finding the geometric mean. Housekeepers can be found using geNorm or NormFinder algorithms
-}
-
-}
 \details{
   Takes expression set of qPCR values and normalises them using a housekeeping gene. Returns a qPCRBatch with exprs set of the same dimensions but with the given hkg value subtracted.
 }

Modified: pkg/NormqPCR/man/deltaDeltaCt.Rd
===================================================================
--- pkg/NormqPCR/man/deltaDeltaCt.Rd	2011-02-15 17:34:49 UTC (rev 127)
+++ pkg/NormqPCR/man/deltaDeltaCt.Rd	2011-02-15 17:59:59 UTC (rev 128)
@@ -8,30 +8,20 @@
 Suitable when housekeeping genes are from same wells/sample as the other detectors
 }
 \usage{
-deltaDeltaCt(qPCRBatch, maxNACase=0, maxNAControl=0, hkgs, contrastM, case, control, paired=TRUE, combineHkgs=FALSE, calc="arith")
+deltaDeltaCt(qPCRBatch, maxNACase=0, maxNAControl=0, hkgs, contrastM, case, control, paired=TRUE, hkgCalc="arith", statCalc="arith")
 }
 \arguments{
-  \item{qPCRBatch}{ Expression set containing qPCR data. 
+  \item{qPCRBatch}{ Expression set containing qPCR data. }
+  \item{maxNACase}{ Maximum number of NA values allowed before a detector's reading is discarded for samples designated as case. }
+  \item{maxNAControl}{ Maximum number of NA values allowed before a detector's reading is discarded for samples designated as control. }
+  \item{hkgs}{ String containing the name of th name of the housekeeping gene which will be used to normalise the rest of the genes. }
+  \item{contrastM}{ A binary matrix which designates case and control samples. }
+  \item{case}{ The name of the column in contrastM that corresponds to the case samples. }
+  \item{control}{ The name of the column in contrastM that corresponds to the control samples. }
+  \item{paired}{ Logical - if TRUE the detectors and housekeepers in the same sample will be paired for calculating standard deviation, effectively meaning we will be calculating standard deviation of the differences. If FALSE, there will be no pairing, and standard deviation will be pooled between the detector and housekeepers. }
+  \item{hkgCalc}{ String - either "arith" or "geom", details how the different housekeeper genes should be combined - either by using the arithmetic or geometric mean. }
+  \item{statCalc}{ String - either "arith" or "geom", details how genes should be combined - either by using the arithmetic or geometric mean. }
 }
-  \item{maxNACase}{ Maximum number of NA values allowed before a detector's reading is discarded for samples designated as case
-}
-  \item{maxNAControl}{ Maximum number of NA values allowed before a detector's reading is discarded for samples designated as control
-}
-  \item{hkgs}{ String containing the name of th name of the housekeeping gene which will be used to normalise the rest of the genes.
-}
-  \item{contrastM}{ A binary matrix which designates case and control samples
-}
-  \item{case}{ The name of the column in contrastM that corresponds to the case samples
-}
-  \item{control}{ The name of the column in contrastM that corresponds to the control samples
-}
-  \item{paired}{ Logical - if TRUE the detectors and housekeepers in the same sample will be paired for calculating standard deviation, effectively meaning we will be calculating standard deviation of the differences. If FALSE, there will be no pairing, and standard deviation will be pooled between the detector and housekeepers
-}
-  \item{combineHkgs}{ Logical - if TRUE, then as long as more than one housekeeper given for argument hkgs, it will combine the housekeepers by finding the mean. Housekeepers can be found using geNorm or NormFinder algorithms
-}
-  \item{calc}{ String - either "arith" or "geom", details how the different housekeeper genes should be combined - either by using the arithmetic or geometric mean
-}
-}
 \details{
   Takes expression set of qPCR values and normalises them using different housekeeping genes. Returns seperate sets of values for each housekeeping gene given.
 }