changed output format to contain FPKM etc. ; fixed a bug for paired-end reads

[rsem.git] / EBSeq / man / GeneEBresultGouldBart2.Rd

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deleted file mode 100644 (file)
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-\name{GeneEBresultGouldBart2}
-\alias{GeneEBresultGouldBart2}
-\docType{data}
-\title{
-The EBSeq result of the empirical gene data ( Gould Lab data, bart2 )
-}
-\description{
-%%  ~~ A concise (1-5 lines) description of the dataset. ~~
-}
-\usage{data(GeneEBresultGouldBart2)}
-\format{
-  The format is:
-List of 17
- $ Alpha   : num [1:5, 1] 0.728 0.724 0.719 0.717 0.717
-  ..- attr(*, "dimnames")=List of 2
-  .. ..$ : chr [1:5] "AlphaIn" "AlphaIn" "AlphaIn" "AlphaIn" ...
-  .. ..$ : NULL
- $ Beta    : num [1:5, 1] 1.44 1.49 1.49 1.49 1.48
-  ..- attr(*, "dimnames")=List of 2
-  .. ..$ : chr [1:5] "BetaIn" "BetaIn" "BetaIn" "BetaIn" ...
-  .. ..$ : NULL
- $ P       : num [1:5, 1] 0.1584 0.0767 0.0534 0.046 0.0432
-  ..- attr(*, "dimnames")=List of 2
-  .. ..$ : chr [1:5] "PIn" "PIn" "PIn" "PIn" ...
-  .. ..$ : NULL
- $ PFromZ  : num [1:5, 1] 0.1585 0.0765 0.0535 0.0459 0.0432
-  ..- attr(*, "dimnames")=List of 2
-  .. ..$ : chr [1:5] "PFromZ" "PFromZ" "PFromZ" "PFromZ" ...
-  .. ..$ : NULL
- $ Z       : Named num [1:15312] 0.0036 0.00246 0.00122 0.61556 0.00394 ...
-  ..- attr(*, "names")= chr [1:15312] "ENSRNOG00000015181" "ENSRNOG00000015180" "ENSRNOG00000027158" "ENSRNOG00000027157" ...
- $ PoissonZ: Named num [1:4955] 6.59e-04 5.71e-04 3.80e-04 2.75e-04 2.07e-05 ...
-  ..- attr(*, "names")= chr [1:4955] "ENSRNOG00000027159" "ENSRNOG00000039120" "ENSRNOG00000039118" "ENSRNOG00000003198" ...
- $ RList   :List of 1
-  ..$ : Named num [1:20267] 19.12 62.3 -3.09 348.78 200.03 ...
-  .. ..- attr(*, "names")= chr [1:20267] "ENSRNOG00000015181" "ENSRNOG00000015180" "ENSRNOG00000027159" "ENSRNOG00000027158" ...
- $ MeanList:List of 1
-  ..$ : Named num [1:20267] 289.663 302.486 0.398 97.791 106.036 ...
-  .. ..- attr(*, "names")= chr [1:20267] "ENSRNOG00000015181" "ENSRNOG00000015180" "ENSRNOG00000027159" "ENSRNOG00000027158" ...
- $ VarList :List of 1
-  ..$ : Named num [1:20267] 5792.7 1954 0.6 146.8 513.4 ...
-  .. ..- attr(*, "names")= chr [1:20267] "ENSRNOG00000015181" "ENSRNOG00000015180" "ENSRNOG00000027159" "ENSRNOG00000027158" ...
- $ QList1  :List of 1
-  ..$ : Named num [1:20267] 0.188 0.152 NaN 0.487 1.118 ...
-  .. ..- attr(*, "names")= chr [1:20267] "ENSRNOG00000015181" "ENSRNOG00000015180" "ENSRNOG00000027159" "ENSRNOG00000027158" ...
- $ QList2  :List of 1
-  ..$ : Named num [1:20267] 0.0389 0.1951 1.1478 1.7647 0.4149 ...
-  .. ..- attr(*, "names")= chr [1:20267] "ENSRNOG00000015181" "ENSRNOG00000015180" "ENSRNOG00000027159" "ENSRNOG00000027158" ...
- $ C1Mean  :List of 1
-  ..$ : Named num [1:20267] 271.9 300.7 0 93.8 123.1 ...
-  .. ..- attr(*, "names")= chr [1:20267] "ENSRNOG00000015181" "ENSRNOG00000015180" "ENSRNOG00000027159" "ENSRNOG00000027158" ...
- $ C2Mean  :List of 1
-  ..$ : Named num [1:20267] 307.414 304.298 0.796 101.798 88.953 ...
-  .. ..- attr(*, "names")= chr [1:20267] "ENSRNOG00000015181" "ENSRNOG00000015180" "ENSRNOG00000027159" "ENSRNOG00000027158" ...
- $ C1EstVar:List of 1
-  ..$ : Named num [1:20267] 1449 1983 0 193 110 ...
-  .. ..- attr(*, "names")= chr [1:20267] "ENSRNOG00000015181" "ENSRNOG00000015180" "ENSRNOG00000027159" "ENSRNOG00000027158" ...
- $ C2EstVar:List of 1
-  ..$ : Named num [1:20267] 7905.417 1559.46 0.694 57.687 214.39 ...
-  .. ..- attr(*, "names")= chr [1:20267] "ENSRNOG00000015181" "ENSRNOG00000015180" "ENSRNOG00000027159" "ENSRNOG00000027158" ...
- $ PoolVar :List of 1
-  ..$ : Named num [1:20267] 4677.246 1771.219 0.347 125.211 162.247 ...
-  .. ..- attr(*, "names")= chr [1:20267] "ENSRNOG00000015181" "ENSRNOG00000015180" "ENSRNOG00000027159" "ENSRNOG00000027158" ...
- $ DataList:List of 1
-  ..$ Ng1: num [1:20267, 1:8] 287 251 0 87 121 181 5 195 70 5 ...
-  .. ..- attr(*, "dimnames")=List of 2
-  .. .. ..$ : chr [1:20267] "I1" "I2" "I3" "I4" ...
-  .. .. ..$ : chr [1:8] "W5-D1" "W5-D2" "W5-D3" "W5-D4" ...
-}
-\details{
-%%  ~~ If necessary, more details than the __description__ above ~~
-}
-\source{
-%%  ~~ reference to a publication or URL from which the data were obtained ~~
-}
-\seealso{
-IsoEBresultGouldBart2, NBBetaEB.bias.uniqueP_PoolVarSpeedUp_MDFPoi_NoNormVar
-}
-\examples{
-data(GeneEBresultGouldBart2)
-## maybe str(GeneEBresultGouldBart2) ; plot(GeneEBresultGouldBart2) ...
-}
-\keyword{datasets}