To see All the content (not just objects) in a package in R

Question

This is likely a newbie's question but I think I did my homework and yet have not found the answer (I hope to find) so I am posting it here to seek some assistance.

Similar questions were asked before but from what I found, no answer could help me with the current issue except an "expensive" solution, which requires an editor for R.

I learned that ls and objects allow us to view the objects inside a package. But even with ls(all.names=TRUE), I still couldn't see all the content. Someone suggested ls(getNAMEspace) but still this isn't "good" enough for me.

e.g.

>search()
[1]".GlobalEvn"      "package:TCGAGBM"
>ls("package:TCGAGBM")
character(0)
>ls(getNamespace("TCGAGBM"),all.names=TRUE)
[1]"._NAMESPACE_."   "._S3MethodsTable_."  ".packageName"

However, under C (cmd), I see the following

C:\Users\XYZ\Documents\R\R-2.15.1\library\TCGAGBM . .. data extdata ...... (total 3 File(s), 7 Dir(s))

I came across this "discrepancy" when I saw the following line of script -

>clinical=read.delim(system.file(
+"extdata/Clinical/clinical_patient_public_GBM.txt.gz",
+package="TCGAGBM"), header=TRUE)

Thus I was wondering if there is a way under R to see ALL the content within a package so that we could "know" how better to utilize the package. Vignette would probably help, but in my limited experience with R so far, I have found that some packages did not come with Vignette.

Any comment will be appreciated to help me learn more about R.

Answer 1

My preferred approach by far is to simply look at the source code of a package in question.

In fact, I actually do that pretty often as running CRANberries creates a local CRAN mirror as a side effect. But even if you don't, CRAN packages really are only a quick download away and will come with comments in the source which the parsed code excludes.

Edit: I just found what Ben found too: Sean Davis' page at http://watson.nci.nih.gov/~sdavis/tutorials/TCGA_data_integration/ -- looks like it uses some BioC packages too. I would still study the source which often has more comments, annotations, extras, ... than the installed package. But maybe that's just my preference. YMMV as they say.

Answer 2

Here is another way to explore the functionality of any package. Although it is not as comprehensive a solution as Dirk's, it is still useful. When I want to know all the functionality of a package, I quickly list all of its functions. Then if I'm curious about any function, I an quickly pull up the help file ?function_name and see what it does. For that reason, I keep this function in my .rprofile so it automatically loads every time I run R.

lsp <- function (package, all.names = FALSE, pattern) {
    package <- deparse(substitute(package))
    ls(pos = paste("package", package, sep = ":"), all.names = all.names, 
        pattern = pattern)
}

This is especially helpful when I know the partial name of a function and what package it belongs to but quickly need to find it.

e.g.

> lsp(ggplot2, pattern = "geom")
 [1] "geom_abline"          "geom_area"           
 [3] "geom_bar"             "geom_bin2d"          
 [5] "geom_blank"           "geom_boxplot"        
 [7] "geom_contour"         "geom_crossbar"       
 [9] "geom_density"         "geom_density2d"      
[11] "geom_dotplot"         "geom_errorbar"       
[13] "geom_errorbarh"       "geom_freqpoly"       
[15] "geom_hex"             "geom_histogram"      
[17] "geom_hline"           "geom_jitter"         
[19] "geom_line"            "geom_linerange"      
[21] "geom_map"             "geom_path"           
[23] "geom_point"           "geom_pointrange"     
[25] "geom_polygon"         "geom_quantile"       
[27] "geom_raster"          "geom_rect"           
[29] "geom_ribbon"          "geom_rug"            
[31] "geom_segment"         "geom_smooth"         
[33] "geom_step"            "geom_text"           
[35] "geom_tile"            "geom_violin"         
[37] "geom_vline"           "update_geom_defaults"

Answer 3

If you want to see all the system files for a particular package, then try something like

list.files(system.file(package = 'TCGAGBM'), recursive = T, full.names = T)

How useful this will be will depend on your OS, as the way packages are installed is OS dependent

see the appropriate section in R Installation and Administration manual for more details.

NOTE

@DirkEddelbuettel's suggestion of inspecting the source is a far better approach.