peptideLibraries {PhIPData} | R Documentation |
PhIP-Seq experiments often use identical peptide libraries different cohorts. These functions enable the user to conveniently reuse tidied libraries.
getLibraryPath() setLibraryPath(path) getLibrary(name) makeLibrary(library, name)
path |
path to a folder containing a .rds files for each library |
name |
name of the library |
library |
a |
Each library is stored as a DataFrame in .rds file.
By default the libraries are stored in the libraries
package folder.
setLibraryPath
allows the user to change the location of this library,
if desired.
While libraries can be directly saved in the specified format by the user,
it is highly recommended to use the makeLibrary
function to
save a new library.
getLibraryPath
returns the path to the directory containing
.rds files for each library. getLibrary
returns a
DataFrame corresponding to the peptide information for the
specified library.
getLibraryPath
: return the path to a folder containing the
libraries.
setLibraryPath
: set the path to a folder containing the
libraries.
getLibrary
: return a DataFrame with the
peptide information corresponding to the library.
makeLibrary
: create and store a DataFrame with
the specified peptide information.
## Get and set path to libraries folder getLibraryPath() ## Not run: setLibraryPath("examplepath/") ## Create a new library pep_meta <- data.frame(species = c(rep("human immunodeficiency virus", 3), rep("Epstein-Barr virus", 2))) makeLibrary(pep_meta, "new_library") ## Use new library counts_dat <- matrix(1:10, nrow = 5) phip_obj <- PhIPData(counts = counts_dat, peptideInfo = getLibrary("new_library")) ## Delete created library file.remove(paste0(getLibraryPath(), "/new_library.rds"))