3 %- Also NEED an '\alias' for EACH other topic documented here.
5 Read in RSEM output of Gould data
8 %% ~~ A concise (1-5 lines) description of what the function does. ~~
11 GetData(path, Name1, Name2, type)
13 %- maybe also 'usage' for other objects documented here.
16 The path of RSEM outputs
19 The output names of the files from Condition 1
22 The output names of the files from Condition 2
25 If type="G", read in the gene level output
26 If type="I", read in the isoform level output
30 %% ~~ If necessary, more details than the description above ~~
33 The output is the "nu values" from RSEM.
34 To generate a expression matrix, the user need to run the PoolMatrix function.
37 %% ~put references to the literature/web site here ~
46 %% ~Make other sections like Warning with \section{Warning }{....} ~
49 %% ~~objects to See Also as \code{\link{help}}, ~~~
52 ##---- Should be DIRECTLY executable !! ----
53 ##-- ==> Define data, use random,
54 ##-- or do help(data=index) for the standard data sets.
56 ## The function is currently defined as
57 function(path,Name1,Name2,type)
65 Filenames=c(Filenames,paste(path,Name1,name,"_isoform_nus.tab",sep=""))
67 Filenames=c(Filenames,paste(path,Name1,name,"_gene_nus.tab",sep=""))
68 Tablenames=c(Tablenames,paste(Name1,name,sep=""))
73 Filenames=c(Filenames,paste(path,Name2,name,"_isoform_nus.tab",sep=""))
75 Filenames=c(Filenames,paste(path,Name2,name,"_gene_nus.tab",sep=""))
76 Tablenames=c(Tablenames,paste(Name2,name,sep=""))
80 names(Data)=Tablenames
83 temp=read.table(Filenames[file],header=T)
84 temp2=as.matrix(temp[-1])
85 rownames(temp2)=as.vector(as.matrix(temp[1]))
91 % Add one or more standard keywords, see file 'KEYWORDS' in the
92 % R documentation directory.
94 \keyword{ ~kwd2 }% __ONLY ONE__ keyword per line