update readme

R/00-utils.R

@@ -24,6 +24,8 @@ setListClass <- function(elementType = NULL, suffix = "List",
     }
 }
 
+
+
 ## Function from IRanges
 .dotargsAsList <- function(...) {
     listData <- list(...)
@@ -95,3 +97,69 @@ addIdNum <- function(x){
         return(x)
     }
 }
+
+## ## How to de-bioc dependencies
+## ## to do define a
+## ## Acknowledgement to S4 vectors, to reduce the dependency, use simple approach
+## ## So far I only need things:
+## ## 1. validation of types
+## ## 2. lappy
+
+
+
+## SList <- setRefClass("SList", 
+##                      fields = list(elementType = "character",
+##                          listData = "list"))
+
+## setMethod("lapply", "SList",
+##           function(X, FUN, ...)
+##               lapply(as.list(X), FUN = FUN, ...))
+
+## setMethod("length", "SList", function(x) length(as.list(x)))
+
+## setMethod("names", "SList", function(x) names(as.list(x)))
+
+## setReplaceMethod("names", "SimpleList",
+##                  function(x, value) {
+##                      names(x@listData) <- value
+##                      x
+##                  })
+
+## setListClass <- function(elementType = NULL, suffix = "List",
+##                          contains = NULL, where = topenv(parent.frame())){
+##     stopifnot(is.character(elementType))
+##     name <- paste0(elementType, suffix)
+##     res <- setRefClass(name, contains = c("SList", contains),
+##                        where = where)
+##     ## setMethod("show", name, function(object){
+##     ##     lapply(object, show)
+##     ## })
+##     function(...){
+##         x <- .dotargsAsList(...)
+##         ## validation
+##         if (!is.list(x)) 
+##             stop("'x' must be a list")
+##         if (is.array(x)) {
+##             tmp_names <- names(x)
+##             dim(x) <- NULL
+##             names(x) <- tmp_names
+##         }
+##         class(x) <- "list"
+##         if (!all(sapply(x,
+##                         function(xi)
+##                             extends(class(xi),
+##                                     elementType)))) 
+##             stop("all elements in 'x' must be ", elementType, 
+##                  " objects")
+##         res(elementType = elementType, listData = x)
+##     }
+## }
+
+## A <- setClass("A", slots = list(x = "character", y = "numeric"))
+## a <- A(x = "a", y = 123)
+
+## AList <- setListClass("A")
+## AList()$elementType
+## lapply(AList(a, a, a), is)
+
+

README.md

@@ -9,7 +9,7 @@ Reference please check
 
 Please pay attention that the github project name is **NOT** `cwl`, but `cwl.R'
 
-### From github
+#### From github
 Directly install from github, need to install Bioc dependency first. 
 
 ```{r}
@@ -19,7 +19,7 @@ biocLite("S4Vectors")
 library(devtools)
 install_github('tengfei/cwl.R')
 ```
-### From Bioconductor
+#### From Bioconductor
 
 When it's on Bioconductor, to install released version
 
@@ -35,3 +35,15 @@ source("http://bioconductor.org/biocLite.R")
 useDevel()
 biocLite("cwl")
 ```
+
+## Use the package
+To load the pacakges
+```{r}
+library(cwl)
+```
+
+To read the vignette
+```{r}
+vignette("cwl-intro")
+```
+