3 %- Also NEED an '\alias' for EACH other topic documented here.
5 Generate the expression matrix from the output of GetData
8 %% ~~ A concise (1-5 lines) description of what the function does. ~~
11 PoolMatrix(Data, reads, type)
13 %- maybe also 'usage' for other objects documented here.
16 The output from GetData function.
19 The total number of reads in each lane. Could be obtained from the RSEM outputs.
22 If type="S", the outputs will be the a matrix which transcript names in row and sample names in column.
23 If type="G", the first column will be the group information.
28 %% ~~ If necessary, more details than the description above ~~
31 \item{PoolM}{The matrix of nu values}
32 \item{PoolValue}{The matrix of expression values}
35 %% ~put references to the literature/web site here ~
44 %% ~Make other sections like Warning with \section{Warning }{....} ~
50 ##---- Should be DIRECTLY executable !! ----
51 ##-- ==> Define data, use random,
52 ##-- or do help(data=index) for the standard data sets.
54 ## The function is currently defined as
55 function(Data,reads,type)
60 poolM=cbind(poolM,Data[[po]][,1])
61 rownames(poolM)=rownames(Data[[1]])
62 colnames(poolM)=poolnames
64 #poolValue=poolM*reads
67 poolValue[,col]=poolM[,col]*reads[col]
68 poolValue=round(poolValue)
71 poolM=cbind(Data[[1]][,2],poolM)
72 poolValue=cbind(Data[[1]][,2],poolValue)
73 colnames(poolM)=c("Groups",poolnames)
74 colnames(poolValue)=c("Groups",poolnames)
76 poolOutput=list(poolM=poolM,poolValue=poolValue)
79 % Add one or more standard keywords, see file 'KEYWORDS' in the
80 % R documentation directory.
82 \keyword{ ~kwd2 }% __ONLY ONE__ keyword per line